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(-) Description

Title :  CRYSTAL STRUCTURE OF IGF-II ANTIBODY COMPLEX
 
Authors :  T. S. Peat, J. Newman, T. E. Adams
Date :  17 Nov 09  (Deposition) - 16 Jun 10  (Release) - 07 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  D,H,L
Keywords :  Antibody-Target Complex, Carbohydrate Metabolism, Glucose Metabolism, Glycoprotein, Growth Factor, Hormone, Mitogen, Osteogenesis, Secreted, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. T. Dransfield, E. H. Cohen, Q. Chang, L. G. Sparrow, J. D. Bentley, O. Dolezal, X. Xiao, T. S. Peat, J. Newman, P. A. Pilling, T. Phan, I. Priebe, G. V. Brierley, N. Kastrapeli, K. Kopacz, D. Martik, D. Wassaf, D. Rank, G. Conley, Y. Huang, T. E. Adams, L. Cosgrove
A Human Monoclonal Antibody Against Insulin-Like Growth Factor-Ii Blocks The Growth Of Human Hepatocellular Carcinoma Cell Lines In Vitro And In Vivo.
Mol. Cancer Ther. V. 9 1809 2010
PubMed-ID: 20515953  |  Reference-DOI: 10.1158/1535-7163.MCT-09-1134

(-) Compounds

Molecule 1 - INSULIN-LIKE GROWTH FACTOR II
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: NOVOZYME PROPRIETARY
    Gene: IGF-II, IGF2, PP1446
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IGF-II, SOMATOMEDIN-A
 
Molecule 2 - ANTIBODY-FAB (HEAVY CHAIN)
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PHAGEMID VECTOR PMID21
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - ANTIBODY-FAB (LIGHT CHAIN)
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PHAGEMID VECTOR PMID21
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : DHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL D:35 , ARG D:40 , SER H:30 , ASN H:31 , SER H:53BINDING SITE FOR RESIDUE EDO H 252
2AC2SOFTWARELEU H:150 , SER H:186 , LEU H:187 , SER H:188 , THR L:179 , HOH L:255BINDING SITE FOR RESIDUE EDO H 253
3AC3SOFTWAREGLY H:9 , GLY H:10 , MET H:117 , THR H:119 , PRO H:156 , GLU H:157 , PRO H:158 , PRO H:211 , HOH H:256 , HOH H:320BINDING SITE FOR RESIDUE EDO H 254
4AC4SOFTWAREPRO L:81 , ARG L:109 , ASP L:171 , SER L:172 , HOH L:291 , HOH L:296BINDING SITE FOR RESIDUE EDO L 216

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1D:9 -D:47
2D:21 -D:60
3D:46 -D:51
4H:22 -H:96
5H:149 -H:205
6L:24 -L:89
7L:135 -L:195

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Phe H:155 -Pro H:156
2Glu H:157 -Pro H:158
3Ser L:8 -Pro L:9
4Ser L:95 -Pro L:96
5Tyr L:141 -Pro L:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KR3)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INSULINPS00262 Insulin family signature.IGF2_HUMAN70-84  1D:46-60

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.7bENST000003813957bENSE00001488507chr11:2158520-2158418103IGF2_HUMAN-00--
1.8ENST000003813958ENSE00002158068chr11:2156759-2156597163IGF2_HUMAN1-53531D:5-2925
1.9bENST000003813959bENSE00001655181chr11:2154895-2154747149IGF2_HUMAN53-102501D:29-6436
1.10iENST0000038139510iENSE00001488587chr11:2154453-21503424112IGF2_HUMAN103-180780--

(-) 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 D from PDB  Type:PROTEIN  Length:60
 aligned with IGF2_HUMAN | P01344 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:60
                                    38        48        58        68        78        88
           IGF2_HUMAN    29 SETLCGGELVDTLQFVCGDRGFYFSRPASRVSRRSRGIVEECCFRSCDLALLETYCATPA  88
               SCOP domains d3kr3d_ D: automated matches                                 SCOP domains
               CATH domains 3kr3D00 D:5-64 Insulin-like, subunit E                       CATH domains
           Pfam domains (1) -------------------------Insulin-3kr3D01 D:30-60        ---- Pfam domains (1)
           Pfam domains (2) -------------------------Insulin-3kr3D02 D:30-60        ---- Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh..hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------INSULIN        ---- PROSITE
           Transcript 1 (1) Exon 1.8  PDB: D:5-29    ----------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------Exon 1.9b  PDB: D:29-64 [INCOMPLETE] Transcript 1 (2)
                 3kr3 D   5 SETLCGGELVDTLQFVCGDRGFYFSRPASRVSRRSRGIVEECCFRSCDLALLETYCATPA  64
                                    14        24        34        44        54        64


Chain H from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3kr3H01 H:1-122 Immunoglobulins                                                                                           3kr3H02 H:123-222 Immunoglobulins                                                              - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee.........eeee...eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kr3 H   1 EVQLLESGGGLVQPGGSLRLSCAASGFTFSNYIMWWVRQAPGKGLEWVSVISSSGGMTRYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDNGDYVGEKGFDIWGQGTMVTVSSASTKGPSVFPLAPSSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      |145       155       165       175       185       195       205       215        
                                                                                                                                                                  137|                                                                                
                                                                                                                                                                   143                                                                                


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains d3kr3l1 L:1-108 automated matches                                                                           d3kr3l2 L:109-214 automated matches                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------3kr3L02 L:109-212 Immunoglobulins                                                                       -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeee....eeeee...hhhhheeeeeee...........eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kr3 L   1 QDIQMTQSPSSLSASVGDRVTITCRASQSISNYLNWYQQKPGKAPKLLIYTASTLQSGVPSRFSGSASGTDFTLTINSLQPEDFATYSCQQSYNSPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTQEDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Insulin (93)

(-) Gene Ontology  (49, 49)

Asymmetric/Biological Unit(hide GO term definitions)
Chain D   (IGF2_HUMAN | P01344)
molecular function
    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:0005179    hormone activity    The action characteristic of a hormone, any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action. The term was originally applied to agents with a stimulatory physiological action in vertebrate animals (as opposed to a chalone, which has a depressant action). Usage is now extended to regulatory compounds in lower animals and plants, and to synthetic substances having comparable effects; all bind receptors and trigger some biological process.
    GO:0005158    insulin receptor binding    Interacting selectively and non-covalently with the insulin receptor.
    GO:0005159    insulin-like growth factor receptor binding    Interacting selectively and non-covalently with the insulin-like 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:0043539    protein serine/threonine kinase activator activity    Binds to and increases the activity of a protein serine/threonine kinase.
    GO:0030546    receptor activator activity    The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    GO:0071260    cellular response to mechanical 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 mechanical stimulus.
    GO:0007565    female pregnancy    The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
    GO:0006006    glucose metabolic process    The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
    GO:0008286    insulin receptor signaling pathway    The series of molecular signals generated as a consequence of the insulin receptor binding to insulin.
    GO:0038028    insulin receptor signaling pathway via phosphatidylinositol 3-kinase    The series of molecular signals generated as a consequence of the insulin receptor binding to its physiological ligand, where the signal is passed on via the phosphatidylinositol 3-kinase cascade.
    GO:0007613    memory    The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task).
    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:0045953    negative regulation of natural killer cell mediated cytotoxicity    Any process that stops, prevents, or reduces the rate of natural killer mediated cytotoxicity.
    GO:0001503    ossification    The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
    GO:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
    GO:0043410    positive regulation of MAPK cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.
    GO:0042104    positive regulation of activated T cell proliferation    Any process that activates or increases the rate or extent of activated T cell proliferation.
    GO:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
    GO:0051781    positive regulation of cell division    Any process that activates or increases the frequency, rate or extent of cell division.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:2000467    positive regulation of glycogen (starch) synthase activity    Any process that activates or increases the frequency, rate or extent of glycogen (starch) synthase activity.
    GO:0045725    positive regulation of glycogen biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen.
    GO:0046628    positive regulation of insulin receptor signaling pathway    Any process that increases the frequency, rate or extent of insulin receptor signaling.
    GO:0045840    positive regulation of mitotic nuclear division    Any process that activates or increases the frequency, rate or extent of mitosis.
    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:0051897    positive regulation of protein kinase B signaling    Any process that activates or increases the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B.
    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:0071902    positive regulation of protein serine/threonine kinase activity    Any process that increases the rate, frequency, or extent of protein serine/threonine kinase activity.
    GO:2000273    positive regulation of receptor activity    Any process that activates or increases the frequency, rate or extent of receptor activity.
    GO:0006349    regulation of gene expression by genetic imprinting    Heritable alterations in the activity of a gene that depend on whether it passed through the paternal or the maternal germline, but that are not encoded by DNA itself.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0042493    response to drug    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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0032355    response to estradiol    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 stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
    GO:0045471    response to ethanol    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 an ethanol stimulus.
    GO:0035094    response to nicotine    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 nicotine stimulus.
    GO:0031667    response to nutrient levels    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 reflecting the presence, absence, or concentration of nutrients.
    GO:0014070    response to organic cyclic compound    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 an organic cyclic compound stimulus.
    GO:0009314    response to radiation    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 an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation.
    GO:0001501    skeletal system development    The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
    GO:0042060    wound healing    The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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: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:0031093    platelet alpha granule lumen    The volume enclosed by the membrane of the platelet alpha granule.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IGF2_HUMAN | P01344: 1gf2 1igl 2l29 2v5p 3e4z 5l3l 5l3m 5l3n

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3KR3)