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(-) Description

Title :  CRYSTAL STRUCTURE OF THE B1B2 DOMAINS FROM HUMAN NEUROPILIN-2
 
Authors :  B. A. Appleton, C. Wiesmann
Date :  26 Jul 07  (Deposition) - 20 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Vegf Receptor, Semaphorin Receptor, Developmental Protein, Differentiation, Glycoprotein, Membrane, Neurogenesis, Transmembrane, Hormone, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. A. Appleton, P. Wu, J. Maloney, J. Yin, W. C. Liang, S. Stawicki, K. Mortara, K. K. Bowman, J. M. Elliott, W. Desmarais, J. F. Bazan, A. Bagri, M. Tessier-Lavigne, A. W. Koch, Y. Wu, R. J. Watts, C. Wiesman
Structural Studies Of Neuropilin/Antibody Complexes Provide Insights Into Semaphorin And Vegf Binding
Embo J. V. 26 4902 2007
PubMed-ID: 17989695  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601906

(-) Compounds

Molecule 1 - NEUROPILIN-2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentF5/8 TYPE C 1 AND C 2 DOMAINS
    GeneNRP2, VEGF165R2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymVASCULAR ENDOTHELIAL CELL GROWTH FACTOR 165 RECEPTOR 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:278 , TYR A:528 , ILE A:538 , GLN A:539 , HOH A:641 , HOH A:690 , HOH A:710 , HOH A:810BINDING SITE FOR RESIDUE GOL A 1

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:277 -A:427
2A:434 -A:592

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2QQJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_067537R334CNRP2_HUMANPolymorphism114144673AR334C
2UniProtVAR_067538R428WNRP2_HUMANPolymorphism139711818AR428W

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FA58C_3PS50022 Coagulation factors 5/8 type C domain (FA58C) profile.NRP2_HUMAN277-427
434-592
  2A:277-427
A:434-592
2FA58C_1PS01285 Coagulation factors 5/8 type C domain (FA58C) signature 1.NRP2_HUMAN317-346
473-505
  2A:317-346
A:473-505
3FA58C_2PS01286 Coagulation factors 5/8 type C domain (FA58C) signature 2.NRP2_HUMAN411-427
575-592
  2A:411-427
A:575-592

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003604092aENSE00001350724chr2:206547224-206548087864NRP2_HUMAN1-25250--
1.4aENST000003604094aENSE00000796618chr2:206562268-206562445178NRP2_HUMAN25-84600--
1.6bENST000003604096bENSE00000796621chr2:206580917-206581098182NRP2_HUMAN84-145620--
1.7bENST000003604097bENSE00000796622chr2:206587202-206587432231NRP2_HUMAN145-222780--
1.8bENST000003604098bENSE00000796624chr2:206588509-206588664156NRP2_HUMAN222-274530--
1.9ENST000003604099ENSE00000796626chr2:206590637-206590806170NRP2_HUMAN274-330571A:276-33055
1.10ENST0000036040910ENSE00000796629chr2:206592615-206592770156NRP2_HUMAN331-382521A:331-38252
1.12ENST0000036040912ENSE00000796630chr2:206605243-206605387145NRP2_HUMAN383-431491A:383-43149
1.13aENST0000036040913aENSE00001238400chr2:206607927-206608276350NRP2_HUMAN431-5471171A:431-547 (gaps)117
1.14ENST0000036040914ENSE00000796635chr2:206610470-206610614145NRP2_HUMAN548-596491A:548-59548
1.15bENST0000036040915bENSE00000796636chr2:206614449-206614565117NRP2_HUMAN596-635400--
1.16bENST0000036040916bENSE00000796638chr2:206617559-206617699141NRP2_HUMAN635-682480--
1.17cENST0000036040917cENSE00000796640chr2:206628398-206628660263NRP2_HUMAN682-769880--
1.19ENST0000036040919ENSE00000796643chr2:206630198-20663029497NRP2_HUMAN770-802330--
1.20bENST0000036040920bENSE00001238223chr2:206631507-20663154236NRP2_HUMAN802-814130--
1.23ENST0000036040923ENSE00000796649chr2:206656959-20665700951NRP2_HUMAN814-831180--
1.24dENST0000036040924dENSE00001350546chr2:206659478-2066628573380NRP2_HUMAN831-9311010--

(-) 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 A from PDB  Type:PROTEIN  Length:315
 aligned with NRP2_HUMAN | O60462 from UniProtKB/Swiss-Prot  Length:931

    Alignment length:320
                                   285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595
           NRP2_HUMAN   276 QCNVPLGMESGRIANEQISASSTYSDGRWTPQQSRLHGDDNGWTPNLDSNKEYLQVDLRFLTMLTAIATQGAISRETQNGYYVKSYKLEVSTNGEDWMVYRHGKNHKVFQANNDATEVVLNKLHAPLLTRFVRIRPQTWHSGIALRLELFGCRVTDAPCSNMLGMLSGLIADSQISASSTQEYLWSPSAARLVSSRSGWFPRIPQAQPGEEWLQVDLGTPKTVKGVIIQGARGGDSITAVEARAFVRKFKVSYSLNGKDWEYIQDPRTQQPKLFEGNMHYDTPDIRRFDPIPAQYVRVYPERWSPAGIGMRLEVLGCDWT 595
               SCOP domains d2qqja1 A:276-433 automated matches                                                                                                                           d2qqja2 A:434-595 automa ted matches                                                                                                                               SCOP domains
               CATH domains 2qqjA01 A:276-430 Galactose-binding domain-like                                                                                                            2qqjA02 A:431-595 Galactose -binding domain-like                                                                                                                      CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------F5_F8_typ e_C-2qqjA01 A:449-589                                                                                                              ------ Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------F5_F8_typ e_C-2qqjA02 A:449-589                                                                                                              ------ Pfam domains (2)
         Sec.struct. author ...ee........hhh.eee.........hhhhh...................eeeeeeeeeeeeeeeee.ee......eeeeeeeeeeee......ee.ee..ee..ee........eeeeeeeeeeeeeeeeeeeeee.....eeeeeeehhhhh...ee........hhh.eee.....-..hhhhhh.....................eeeeeeeeeeeeeeeee.....----.......eeeeeeeee......ee.ee....ee..ee........eeeeeeeeeeeeeeeeeeee.......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------C---------------------------------------------------------------------------------------------W----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -FA58C_3  PDB: A:277-427 UniProt: 277-427                                                                                                               ------FA58C_3  PDB: A:434-592 UniProt: 434-592                                                                                                                       --- PROSITE (1)
                PROSITE (2) -----------------------------------------FA58C_1  PDB: A:317-346       ----------------------------------------------------------------FA58C_2          ---------------------------------------------FA58C_1  PDB: A:473-505          ---------------------------------------------------------------------FA58C_2           --- PROSITE (2)
           Transcript 1 (1) Exon 1.9  PDB: A:276-330 UniProt: 274-330 [INCOMPLETE] Exon 1.10  PDB: A:331-382 UniProt: 331-382          Exon 1.12  PDB: A:383-431 UniProt: 383-431       --------------------------------------------------------------------------------------------------------------------Exon 1.14  PDB: A:548-595 UniProt: 548-596       Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.13a  PDB: A:431-547 (gaps) UniProt: 431-547                                                                   ------------------------------------------------ Transcript 1 (2)
                 2qqj A 276 QCNVPLGMESGRIANEQISASSTYSDGRWTPQQSRLHGDDNGWTPNLDSNKEYLQVDLRFLTMLTAIATQGAISRETQNGYYVKSYKLEVSTNGEDWMVYRHGKNHKVFQANNDATEVVLNKLHAPLLTRFVRIRPQTWHSGIALRLELFGCRVTDAPCSNMLGMLSGLIADSQISASSTQE-LWSPSAARLVSSRSGWFPRIPQAQPGEEWLQVDLGTPKTVKGVIIQGARGG----AVEARAFVRKFKVSYSLNGKDWEYIQDPRTQQPKLFEGNMHYDTPDIRRFDPIPAQYVRVYPERWSPAGIGMRLEVLGCDWT 595
                                   285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455 | |   465       475       485       495       505   |   515       525       535       545       555       565       575       585       595
                                                                                                                                                                                                               457 |                                               509  514                                                                                 
                                                                                                                                                                                                                 459                                                                                                                                        

   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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: GBD (153)

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NRP2_HUMAN | O60462)
molecular function
    GO:0019955    cytokine binding    Interacting selectively and non-covalently with a cytokine, any of a group of proteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity.
    GO:0019838    growth factor binding    Interacting selectively and non-covalently with any growth factor, proteins or polypeptides that stimulate a cell or organism to grow or proliferate.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    GO:0017154    semaphorin receptor activity    Combining with a semaphorin, and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
    GO:0005021    vascular endothelial growth factor-activated receptor activity    Combining with a vascular endothelial growth factor (VEGF) and transmitting the signal across the plasma membrane to initiate a change in cell activity.
biological process
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0048846    axon extension involved in axon guidance    The long distance growth of a single cell process, that is involved in the migration of an axon growth cone, where the migration is directed to a specific target site by a combination of attractive and repulsive cues.
    GO:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    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: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:0021675    nerve development    The process whose specific outcome is the progression of a nerve over time, from its formation to the mature structure.
    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: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:1902285    semaphorin-plexin signaling pathway involved in neuron projection guidance    Any semaphorin-plexin signaling pathway that is involved in neuron projection guidance.
    GO:0061549    sympathetic ganglion development    The process whose specific outcome is the progression of a sympathetic ganglion over time, from its formation to the mature structure.
    GO:0097490    sympathetic neuron projection extension    Long distance growth of a single sympathetic neuron projection involved in cellular development. A neuron projection is a prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0097491    sympathetic neuron projection guidance    The process in which the migration of a sympathetic neuron projection is directed to a specific target site in response to a combination of attractive and repulsive cues.
    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.
cellular component
    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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0002116    semaphorin receptor complex    A stable binary complex of a neurophilin and a plexin, together forming a functional semaphorin receptor.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NRP2_HUMAN | O604622qqk 2qql 2qqo 4qdq 4qdr 4qds 5dn2 5dq0

(-) Related Entries Specified in the PDB File

2qqi 2qqk 2qql 2qqm 2qqn 2qqo