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(-) Description

Title :  VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH A NEUTRALIZING ANTIBODY
 
Authors :  Y. A. Muller, H. W. Christinger, A. M. De Vos
Date :  30 Jun 98  (Deposition) - 13 Jan 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  H,J,K,L,V,W
Keywords :  Complex (Antibody/Antigen), Angiogenic Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. A. Muller, Y. Chen, H. W. Christinger, B. Li, B. C. Cunningham, H. B. Lowman, A. M. De Vos
Vegf And The Fab Fragment Of A Humanized Neutralizing Antibody: Crystal Structure Of The Complex At 2. 4 A Resolution And Mutational Analysis Of The Interface.
Structure V. 6 1153 1998
PubMed-ID: 9753694  |  Reference-DOI: 10.1016/S0969-2126(98)00116-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FAB FRAGMENT
    ChainsL, J
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsHUMANIZED VERSION OF A MONOCLONAL MURINE ANTI-VEGF ANTIBODY
    Other Details - SourceHUMANIZED VERSION OF A MONOCLONAL MURINE ANTI-VEGF ANTIBODY
    SynonymFAB-12
 
Molecule 2 - FAB FRAGMENT
    ChainsH, K
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsHUMANIZED VERSION OF A MONOCLONAL MURINE ANTI-VEGF ANTIBODY
    Other Details - SourceHUMANIZED VERSION OF A MONOCLONAL MURINE ANTI-VEGF ANTIBODY
    SynonymFAB-12
 
Molecule 3 - VASCULAR ENDOTHELIAL GROWTH FACTOR
    ChainsV, W
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRECEPTOR BINDING DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymVEGF

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit HJKLVW

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR H:28 , ASN H:31 , TYR H:32 , HOH H:368 , ILE W:91 , HOH W:111BINDING SITE FOR RESIDUE SO4 H 232
2AC2SOFTWARETYR K:27 , THR K:28 , ASN K:31 , TYR K:32 , ILE V:91 , HOH V:112BINDING SITE FOR RESIDUE SO4 K 232

(-) SS Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:96
2J:134 -J:194
3L:134 -L:194
4V:26 -V:68
5V:57 -V:102
6V:61 -V:104
7W:26 -W:68
8W:57 -W:102
9W:61 -W:104

(-) Cis Peptide Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Val L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Phe H:156 -Pro H:157
5Glu H:158 -Pro H:159
6Lys V:48 -Pro V:49
7Lys W:48 -Pro W:49
8Ser J:7 -Pro J:8
9Val J:94 -Pro J:95
10Tyr J:140 -Pro J:141
11Phe K:156 -Pro K:157
12Glu K:158 -Pro K:159

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BJ1)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDGF_1PS00249 Platelet-derived growth factor (PDGF) family signature.VEGFA_HUMAN75-87
 
  2V:49-61
W:49-61

(-) Exons   (0, 0)

(no "Exon" information available for 1BJ1)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain H from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains d1bj1h1 H:1-123 Immunoglobulin heavy chain variable domain, VH                                                             d1bj1h2 H:124-224 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                 SCOP domains
               CATH domains 1bj1H01 H:1-123 Immunoglobulins                                                                                            1bj1H02 H:124-223 Immunoglobulins                                                             - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee...hhh..eeeeee......eeeeee......eee.hhh...eeeeeehhh.eeeeee....hhh.eeeeeeee..........eeee...eeeee........eeeee....eeeeeeeeeee.....eeeehhh.....eee..........eeeeeeeeee.........eeeeeehhh.eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bj1 H   1 EVQLVESGGGLVQPGGSLRLSCAASGYTFTNYGMNWVRQAPGKGLEWVGWINTYTGEPTYAADFKRRFTFSLDTSKSTAYLQMNSLRAEDTAVYYCAKYPHYYGSSHWYFDVWGQGTLVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      |146       156       166       176       186       196       206       216        
                                                                                                                                                                  137|                                                                                
                                                                                                                                                                   144                                                                                

Chain J from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d1bj1j1 J:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1bj1j2 J:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1bj1J01 J:1-108 Immunoglobulins                                                                             1bj1J02 J:109-211 Immunoglobulins                                                                      -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeee.............eeeeee..eeeeee....hhh.eeeeeee...........eeeee.......eeeee...hhhhhh.eeeeeeeee......eeeeeee........eeeee...........eeeeeeeehhhh....eeeeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bj1 J   1 DIQMTQSPSSLSASVGDRVTITCSASQDISNYLNWYQQKPGKAPKVLIYFTSSLHSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYSTVPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   

Chain K from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains d1bj1k1 K:1-123 Immunoglobulin heavy chain variable domain, VH                                                             d1bj1k2 K:124-224 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                 SCOP domains
               CATH domains 1bj1K01 K:1-123 Immunoglobulins                                                                                            1bj1K02 K:124-223 Immunoglobulins                                                             - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee...hhh..eeeeee......eeeeee......eee.hhh...eeeeee....eeeeee....hhh.eeeeeeee..........eeee...eeeee........eeeee....eeeeeeeeeee.....eeeehhh..................eeeeeeeeee.hhhh...eeeeee.hhh....eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bj1 K   1 EVQLVESGGGLVQPGGSLRLSCAASGYTFTNYGMNWVRQAPGKGLEWVGWINTYTGEPTYAADFKRRFTFSLDTSKSTAYLQMNSLRAEDTAVYYCAKYPHYYGSSHWYFDVWGQGTLVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      |146       156       166       176       186       196       206       216        
                                                                                                                                                                  137|                                                                                
                                                                                                                                                                   144                                                                                

Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d1bj1l1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1bj1l2 L:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1bj1L01 L:1-108 Immunoglobulins                                                                             1bj1L02 L:109-211 Immunoglobulins                                                                      -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeee.............eeeeee..eeeeee....hhh.eeeeeee...........eeeeee......eeeee...hhhhhh.eeeeeeeee.......eeeeee........eeeee...........eeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bj1 L   1 DIQMTQSPSSLSASVGDRVTITCSASQDISNYLNWYQQKPGKAPKVLIYFTSSLHSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYSTVPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   

Chain V from PDB  Type:PROTEIN  Length:94
 aligned with VEGFA_HUMAN | P15692 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:94
                                    49        59        69        79        89        99       109       119       129    
          VEGFA_HUMAN    40 VVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPK 133
               SCOP domains d1bj1v_ V: Vascular endothelial growth factor, VEGF                                            SCOP domains
               CATH domains 1bj1V00 V:14-107 Cystine-knot cytokines                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh..eeeeeeeehhhh.......eee..eeeeeeee.......eeeeeeeeeeeeeeeeeee...eeeeeeeeeeee.eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------PDGF_1       ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 1bj1 V  14 VVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPK 107
                                    23        33        43        53        63        73        83        93       103    

Chain W from PDB  Type:PROTEIN  Length:94
 aligned with VEGFA_HUMAN | P15692 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:94
                                    49        59        69        79        89        99       109       119       129    
          VEGFA_HUMAN    40 VVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPK 133
               SCOP domains d1bj1w_ W: Vascular endothelial growth factor, VEGF                                            SCOP domains
               CATH domains 1bj1W00 W:14-107 Cystine-knot cytokines                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh..eeeeeeeehhhh.......eee..eeeeeeee.......eeeeeeeeeeeeeeeeeee...eeeeeeeeeeee.eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------PDGF_1       ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 1bj1 W  14 VVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPK 107
                                    23        33        43        53        63        73        83        93       103    

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (5, 10)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 10)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BJ1)

(-) Gene Ontology  (122, 122)

Asymmetric/Biological Unit(hide GO term definitions)
Chain V,W   (VEGFA_HUMAN | P15692)
molecular function
    GO:0042056    chemoattractant activity    Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a higher concentration of that signal.
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0050840    extracellular matrix binding    Interacting selectively and non-covalently with a component of the extracellular matrix.
    GO:0001968    fibronectin binding    Interacting selectively and non-covalently with a fibronectin, a group of related adhesive glycoproteins of high molecular weight found on the surface of animal cells, connective tissue matrices, and in extracellular fluids.
    GO:0008083    growth factor activity    The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0038191    neuropilin binding    Interacting selectively and non-covalently with a member of the neuropilin family.
    GO:0005161    platelet-derived growth factor receptor binding    Interacting selectively and non-covalently with the platelet-derived growth factor receptor.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0048018    receptor agonist activity    Interacts with receptors such that the proportion of receptors in the active form is increased.
    GO:0043183    vascular endothelial growth factor receptor 1 binding    Interacting selectively and non-covalently with vascular endothelial growth factor receptor 1.
    GO:0043184    vascular endothelial growth factor receptor 2 binding    Interacting selectively and non-covalently with vascular endothelial growth factor receptor 2.
    GO:0005172    vascular endothelial growth factor receptor binding    Interacting selectively and non-covalently with any vascular endothelial growth factor receptor.
biological process
    GO:0038190    VEGF-activated neuropilin signaling pathway    A series of molecular signals initiated by the binding of vascular endothelial growth factor (VEGF) to a neuropilin protein on the surface of a target cell, followed by transmission of the signal, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0032147    activation of protein kinase activity    Any process that initiates the activity of an inactive protein kinase.
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0048844    artery morphogenesis    The process in which the anatomical structures of arterial blood vessels are generated and organized. Arteries are blood vessels that transport blood from the heart to the body and its organs.
    GO:0002575    basophil chemotaxis    The movement of a basophil in response to an external stimulus.
    GO:0001569    branching involved in blood vessel morphogenesis    The process of coordinated growth and sprouting of blood vessels giving rise to the organized vascular system.
    GO:0048754    branching morphogenesis of an epithelial tube    The process in which the anatomical structures of branches in an epithelial tube are generated and organized. A tube is a long hollow cylinder.
    GO:0048593    camera-type eye morphogenesis    The process in which the anatomical structures of the eye are generated and organized. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field.
    GO:0048739    cardiac muscle fiber development    The process whose specific outcome is the progression of cardiac muscle fiber over time, from its formation to the mature structure.
    GO:0060948    cardiac vascular smooth muscle cell development    The process whose specific outcome is the progression of a cardiac vascular smooth muscle cell over time, from its formation to the mature state.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0048469    cell maturation    A developmental process, independent of morphogenetic (shape) change, that is required for a cell to attain its fully functional state.
    GO:0002042    cell migration involved in sprouting angiogenesis    The orderly movement of endothelial cells into the extracellular matrix in order to form new blood vessels involved in sprouting angiogenesis.
    GO:0071456    cellular response to hypoxia    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0035924    cellular response to vascular endothelial growth factor stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vascular endothelial growth factor stimulus.
    GO:0071679    commissural neuron axon guidance    The process in which the migration of an axon growth cone of a commissural neuron is directed to its target in the brain in response to a combination of attractive and repulsive cues.
    GO:0060982    coronary artery morphogenesis    The process in which the anatomical structures of coronary arteries are generated and organized. Coronary arteries are blood vessels that transport blood to the heart muscle.
    GO:0003169    coronary vein morphogenesis    The process in which the anatomical structures of veins of the heart are generated and organized.
    GO:0071542    dopaminergic neuron differentiation    The process in which a neuroblast acquires the specialized structural and functional features of a dopaminergic neuron, a neuron that secretes dopamine.
    GO:0035767    endothelial cell chemotaxis    The directed movement of an endothelial cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0030855    epithelial cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium.
    GO:0042462    eye photoreceptor cell development    Development of a photoreceptor, a sensory cell in the eye that reacts to the presence of light. They usually contain a pigment that undergoes a chemical change when light is absorbed, thus stimulating a nerve.
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:0003007    heart morphogenesis    The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0050930    induction of positive chemotaxis    Any process that initiates the directed movement of a motile cell or organism towards a higher concentration in a concentration gradient of a specific chemical.
    GO:0001822    kidney development    The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.
    GO:0007595    lactation    The regulated release of milk from the mammary glands and the period of time that a mother lactates to feed her young.
    GO:0030324    lung development    The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
    GO:0036303    lymph vessel morphogenesis    The process in which the anatomical structures of lymph vessels are generated and organized. The lymph vessel is the vasculature carrying lymph.
    GO:0030225    macrophage differentiation    The process in which a relatively unspecialized monocyte acquires the specialized features of a macrophage.
    GO:0060749    mammary gland alveolus development    The progression of the mammary gland alveolus over time, from its formation to its mature state. The mammary gland alveolus is a sac-like structure that is found in the mature gland.
    GO:0007498    mesoderm development    The process whose specific outcome is the progression of the mesoderm over time, from its formation to the mature structure. The mesoderm is the middle germ layer that develops into muscle, bone, cartilage, blood and connective tissue.
    GO:0030224    monocyte differentiation    The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a monocyte.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0043154    negative regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0003151    outflow tract morphogenesis    The process in which the anatomical structures of the outflow tract are generated and organized. The outflow tract is the portion of the heart through which blood flows into the arteries.
    GO:0001541    ovarian follicle development    The process whose specific outcome is the progression of the ovarian follicle over time, from its formation to the mature structure.
    GO:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
    GO:0050918    positive chemotaxis    The directed movement of a motile cell or organism towards a higher concentration of a chemical.
    GO:0032793    positive regulation of CREB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor CREB.
    GO:0070374    positive regulation of ERK1 and ERK2 cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0043406    positive regulation of MAP kinase activity    Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
    GO:0045766    positive regulation of angiogenesis    Any process that activates or increases angiogenesis.
    GO:0048842    positive regulation of axon extension involved in axon guidance    Any process that activates, maintains or increases the frequency, rate or extent of axon extension involved in axon guidance.
    GO:0043536    positive regulation of blood vessel endothelial cell migration    Any process that activates or increases the frequency, rate or extent of the migration of the endothelial cells of blood vessels.
    GO:0090190    positive regulation of branching involved in ureteric bud morphogenesis    Any process that increases the rate, frequency or extent of branching involved in ureteric bud morphogenesis, the process in which the branching structure of the ureteric bud is generated and organized. The ureteric bud is an epithelial tube that grows out from the metanephric duct. The bud elongates and branches to give rise to the ureter and kidney collecting tubules.
    GO:0045785    positive regulation of cell adhesion    Any process that activates or increases the frequency, rate or extent of cell adhesion.
    GO:0051781    positive regulation of cell division    Any process that activates or increases the frequency, rate or extent of cell division.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0090050    positive regulation of cell migration involved in sprouting angiogenesis    Any process that increases the frequency, rate or extent of cell migration involved in sprouting angiogenesis. Cell migration involved in sprouting angiogenesis is the orderly movement of endothelial cells into the extracellular matrix in order to form new blood vessels contributing to the process of sprouting angiogenesis.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0038091    positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway    A series of molecular signals initiated by the binding of a vascular endothelial growth factor (VEGF) to a platelet-derived growth factor receptor (PDGFR) on the surface of a cell, which activates or increases the frequency, rate or extent of cell proliferation.
    GO:0051272    positive regulation of cellular component movement    Any process that activates or increases the frequency, rate or extent of the movement of a cellular component.
    GO:0038033    positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway    A series of molecular signals initiated by the binding of a vascular endothelial growth factor (VEGF) to a VEGFR on the surface of a cell, which activates or increases the frequency, rate or extent of endothelial cell chemotaxis.
    GO:0010595    positive regulation of endothelial cell migration    Any process that increases the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
    GO:0001938    positive regulation of endothelial cell proliferation    Any process that activates or increases the rate or extent of endothelial cell proliferation.
    GO:0050679    positive regulation of epithelial cell proliferation    Any process that activates or increases the rate or extent of epithelial cell proliferation.
    GO:0051894    positive regulation of focal adhesion assembly    Any process that activates or increases the frequency, rate or extent of focal adhesion assembly, the establishment and maturation of focal adhesions.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:1901727    positive regulation of histone deacetylase activity    Any process that activates or increases the frequency, rate or extent of histone deacetylase activity.
    GO:0002687    positive regulation of leukocyte migration    Any process that activates or increases the frequency, rate, or extent of leukocyte migration.
    GO:0060754    positive regulation of mast cell chemotaxis    Any process that increases the rate, frequency or extent of mast cell chemotaxis. Mast cell chemotaxis is the movement of a mast cell in response to an external stimulus.
    GO:0002053    positive regulation of mesenchymal cell proliferation    The process of activating or increasing the rate or extent of mesenchymal cell proliferation. Mesenchymal cells are loosely organized embryonic cells.
    GO:0002052    positive regulation of neuroblast proliferation    Any process that activates or increases the rate of neuroblast proliferation.
    GO:1900745    positive regulation of p38MAPK cascade    Any process that activates or increases the frequency, rate or extent of p38MAPK cascade.
    GO:0033138    positive regulation of peptidyl-serine phosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-serine.
    GO:1900086    positive regulation of peptidyl-tyrosine autophosphorylation    Any process that activates or increases the frequency, rate or extent of peptidyl-tyrosine autophosphorylation.
    GO:0050731    positive regulation of peptidyl-tyrosine phosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
    GO:0050927    positive regulation of positive chemotaxis    Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism towards a higher concentration in a concentration gradient of a specific chemical.
    GO:0031954    positive regulation of protein autophosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation by a protein of one or more of its own residues.
    GO:0031334    positive regulation of protein complex assembly    Any process that activates or increases the frequency, rate or extent of protein complex assembly.
    GO:0090037    positive regulation of protein kinase C signaling    Any process that increases the frequency, rate, or extent of a series of reactions, mediated by the intracellular serine/threonine kinase protein kinase C, which occurs as a result of a single trigger reaction or compound.
    GO:1903572    positive regulation of protein kinase D signaling    Any process that activates or increases the frequency, rate or extent of protein kinase D signaling.
    GO:1902966    positive regulation of protein localization to early endosome    Any process that activates or increases the frequency, rate or extent of protein localization to early endosome.
    GO:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    GO:0002092    positive regulation of receptor internalization    Any process that activates or increases the frequency, rate or extent of receptor internalization.
    GO:1902336    positive regulation of retinal ganglion cell axon guidance    Any process that activates or increases the frequency, rate or extent of retinal ganglion cell axon guidance.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0061419    positive regulation of transcription from RNA polymerase II promoter in response to hypoxia    Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus.
    GO:0030949    positive regulation of vascular endothelial growth factor receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of vascular endothelial growth factor receptor signaling pathway activity.
    GO:0043117    positive regulation of vascular permeability    Any process that increases the extent to which blood vessels can be pervaded by fluid.
    GO:0031077    post-embryonic camera-type eye development    The process occurring during the post-embryonic phase whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure.
    GO:0060319    primitive erythrocyte differentiation    Erythrocyte differentiation which occurs as part of the process of primitive hemopoiesis.
    GO:0030823    regulation of cGMP metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving cGMP.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0090259    regulation of retinal ganglion cell axon guidance    Any process that modulates the frequency, rate, or extent of retinal ganglion cell axon guidance, the process in which the migration of an axon growth cone of a retinal ganglion cell (RGC) is directed to its target in the brain in response to a combination of attractive and repulsive cues.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0061418    regulation of transcription from RNA polymerase II promoter in response to hypoxia    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus.
    GO:0001666    response to hypoxia    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0043129    surfactant homeostasis    Any process involved in the maintenance of a steady-state level of the surface-active lipoprotein mixture which coats the alveoli.
    GO:0035148    tube formation    Creation of the central hole of a tube in an anatomical structure through which gases and/or liquids flow.
    GO:0048010    vascular endothelial growth factor receptor signaling pathway    Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor (VEGFR) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0038084    vascular endothelial growth factor signaling pathway    A series of molecular signals initiated by the binding of a vascular endothelial growth factor (VEGF) to a receptor on the surface of the target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0001570    vasculogenesis    The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0031093    platelet alpha granule lumen    The volume enclosed by the membrane of the platelet alpha granule.
    GO:0005578    proteinaceous extracellular matrix    A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.
    GO:0030141    secretory granule    A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        VEGFA_HUMAN | P156921cz8 1flt 1kat 1kmx 1mjv 1mkg 1mkk 1qty 1tzh 1tzi 1vgh 1vpf 1vpp 2fjg 2fjh 2qr0 2vgh 2vpf 3bdy 3p9w 3qtk 3s1b 3s1k 3v2a 4deq 4gln 4gls 4kzn 4qaf 4wpb 4zff 5dn2 5fv1 5fv2 5hhc 5hhd 5t89

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1BJ1)