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(-) Description

Title :  GRB7 SH2 WITH PEPTIDE
 
Authors :  J. A. Wilce
Date :  29 Nov 10  (Deposition) - 20 Jul 11  (Release) - 21 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.41
Chains :  Asym. Unit :  A,B,C,D,L,M
Biol. Unit 1:  A,D,L  (1x)
Biol. Unit 2:  B,C,M  (1x)
Keywords :  Sh2, Binds Phosphotyrosine, Tyrosine Kinases, Cytoplasmic, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. D. Ambaye, S. C. Pero, M. J. Gunzburg, M. Yap, D. J. Clayton, M. P. Del Borgo, P. Perlmutter, M. I. Aguilar, G. S. Shukla, E. Peletskaya, M. M. Cookson, D. N. Krag, M. C. Wilce, J. A. Wilce
Structural Basis Of Binding By Cyclic Nonphosphorylated Peptide Antagonists Of Grb7 Implicated In Breast Cancer Progression
J. Mol. Biol. V. 412 397 2011
PubMed-ID: 21802427  |  Reference-DOI: 10.1016/J.JMB.2011.07.030

(-) Compounds

Molecule 1 - GROWTH FACTOR RECEPTOR-BOUND PROTEIN 7
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSH2 DOMAIN
    GeneGRB7
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymB47, EPIDERMAL GROWTH FACTOR RECEPTOR GRB-7, GRB7 ADAPTER PROTEIN
 
Molecule 2 - CYCLIC PEPTIDE
    ChainsL, M
    EngineeredYES
    Other DetailsSEQUENCE DESIGNED BY PHASE DISPLAY. PEPTIDE WAS MADE SYNTHETICALLY
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDLM
Biological Unit 1 (1x)A  DL 
Biological Unit 2 (1x) BC  M

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CCS2Mod. Amino AcidCARBOXYMETHYLATED CYSTEINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CCS1Mod. Amino AcidCARBOXYMETHYLATED CYSTEINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CCS1Mod. Amino AcidCARBOXYMETHYLATED CYSTEINE

(-) Sites  (0, 0)

(no "Site" information available for 3PQZ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PQZ)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:488 -Gly A:489
2Gln D:461 -Arg D:462

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.GRB7_HUMAN431-527
 
 
 
  4A:431-527
B:431-527
C:431-527
D:431-527
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.GRB7_HUMAN431-527
 
 
 
  2A:431-527
-
-
D:431-527
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH2PS50001 Src homology 2 (SH2) domain profile.GRB7_HUMAN431-527
 
 
 
  2-
B:431-527
C:431-527
-

(-) Exons   (4, 14)

Asymmetric Unit (4, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000003942112ENSE00001517752chr17:37894576-3789464570GRB7_HUMAN-00--
1.4aENST000003942114aENSE00002183795chr17:37898505-37898709205GRB7_HUMAN1-52520--
1.5aENST000003942115aENSE00001227713chr17:37898819-37898969151GRB7_HUMAN52-102510--
1.5dENST000003942115dENSE00000950638chr17:37899151-37899307157GRB7_HUMAN103-155530--
1.6aENST000003942116aENSE00000950639chr17:37899433-37899554122GRB7_HUMAN155-195410--
1.6dENST000003942116dENSE00000950640chr17:37899646-3789972378GRB7_HUMAN196-221260--
1.7aENST000003942117aENSE00000950641chr17:37900323-37900460138GRB7_HUMAN222-267460--
1.8ENST000003942118ENSE00000950642chr17:37900806-37900916111GRB7_HUMAN268-304370--
1.9ENST000003942119ENSE00000950643chr17:37901139-3790123799GRB7_HUMAN305-337330--
1.10ENST0000039421110ENSE00000950644chr17:37901496-3790157681GRB7_HUMAN338-364270--
1.11ENST0000039421111ENSE00000950645chr17:37901675-37901791117GRB7_HUMAN365-403390--
1.12ENST0000039421112ENSE00000950646chr17:37901981-3790204161GRB7_HUMAN404-424212A:424-424
B:423-424
-
-
1
2
-
-
1.13ENST0000039421113ENSE00000950647chr17:37902166-3790225388GRB7_HUMAN424-453304A:424-453
B:424-453
C:430-453
D:429-453
30
30
24
25
1.14ENST0000039421114ENSE00001651412chr17:37902362-3790245594GRB7_HUMAN453-484324A:453-484 (gaps)
B:453-484 (gaps)
C:453-484
D:453-484
32
32
32
32
1.15cENST0000039421115cENSE00001850980chr17:37903004-37903538535GRB7_HUMAN485-532484A:485-528
B:485-529 (gaps)
C:485-527 (gaps)
D:485-527 (gaps)
44
45
43
43

(-) Sequences/Alignments

Asymmetric 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:104
 aligned with GRB7_HUMAN | Q14451 from UniProtKB/Swiss-Prot  Length:532

    Alignment length:105
                                   433       443       453       463       473       483       493       503       513       523     
           GRB7_HUMAN   424 AIHRTQLWFHGRISREESQRLIGQQGLVDGLFLVRESQRNPQGFVLSLCHLQKVKHYLILPSEEEGRLYFSMDDGQTRFTDLLQLVEFHQLNRGILPCLLRHCCT 528
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.......hhhhhhhhhhhh.....eeeeee...-...eeeeeee..eeeeeeeeee......eee.........hhhhhhhhhhhh.........ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------SH2  PDB: A:431-527 UniProt: 431-527                                                             - PROSITE
           Transcript 1 (1) 1----------------------------Exon 1.14  PDB: A:453-484 (gaps)Exon 1.15c  PDB: A:485-528 UniProt: 485-532  Transcript 1 (1)
           Transcript 1 (2) Exon 1.13  PDB: A:424-453     --------------------------------------------------------------------------- Transcript 1 (2)
                 3pqz A 424 AIHRTQLWFHGRISREESQRLIGQQGLVDGLFLVRESQR-PQGFVLSLCHLQKVKHYLILPSEEEGRLYFSMDDGQTRFTDLLQLVEFHQLNRGILPCLLRHCCT 528
                                   433       443       453        |-|      473       483       493       503       513       523     
                                                                462 |                                                                
                                                                  464                                                                

Chain B from PDB  Type:PROTEIN  Length:105
 aligned with GRB7_HUMAN | Q14451 from UniProtKB/Swiss-Prot  Length:532

    Alignment length:107
                                   432       442       452       462       472       482       492       502       512       522       
           GRB7_HUMAN   423 AAIHRTQLWFHGRISREESQRLIGQQGLVDGLFLVRESQRNPQGFVLSLCHLQKVKHYLILPSEEEGRLYFSMDDGQTRFTDLLQLVEFHQLNRGILPCLLRHCCTR 529
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhh.....eeeeee....-..eeeeeee..eeeeeeeeee..-...eee.........hhhhhhhhhhhh.........ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------SH2  PDB: B:431-527 UniProt: 431-527                                                             -- PROSITE
           Transcript 1 (1) 1.----------------------------Exon 1.14  PDB: B:453-484 (gaps)Exon 1.15c  PDB: B:485-529 (gaps)             Transcript 1 (1)
           Transcript 1 (2) -Exon 1.13  PDB: B:424-453     ---------------------------------------------------------------------------- Transcript 1 (2)
                 3pqz B 423 AAIHRTQLWFHGRISREESQRLIGQQGLVDGLFLVRESQRN-QGFVLSLCHLQKVKHYLILPSEE-GRLYFSMDDGQTRFTDLLQLVEFHQLNRGILPCLLRHCCTR 529
                                   432       442       452       462| |    472       482    | |492       502       512       522       
                                                                  463 |                   487 |                                        
                                                                    465                     489                                        

Chain C from PDB  Type:PROTEIN  Length:97
 aligned with GRB7_HUMAN | Q14451 from UniProtKB/Swiss-Prot  Length:532

    Alignment length:98
                                   439       449       459       469       479       489       499       509       519        
           GRB7_HUMAN   430 LWFHGRISREESQRLIGQQGLVDGLFLVRESQRNPQGFVLSLCHLQKVKHYLILPSEEEGRLYFSMDDGQTRFTDLLQLVEFHQLNRGILPCLLRHCC 527
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhh.....eeeeee.......eeeeee....eeeeeeeeee..-.eeee.........hhhhhhhhhhhh.........ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -SH2  PDB: C:431-527 UniProt: 431-527                                                              PROSITE
           Transcript 1 (1) -----------------------Exon 1.14  PDB: C:453-484       Exon 1.15c  PDB: C:485-527 (gaps)           Transcript 1 (1)
           Transcript 1 (2) Exon 1.13  PDB: C:430-45-------------------------------------------------------------------------- Transcript 1 (2)
                 3pqz C 430 LWFHGRISREESQRLIGQQGLVDGLFLVRESQRNPQGFVLSLCHLQKVKHYLILPSEEE-RLYFSMDDGQTRFTDLLQLVEFHQLNRGILPCLLRHCC 527
                                   439       449       459       469       479        |-|      499       509       519        
                                                                                    488 |                                     
                                                                                      490                                     

Chain D from PDB  Type:PROTEIN  Length:97
 aligned with GRB7_HUMAN | Q14451 from UniProtKB/Swiss-Prot  Length:532

    Alignment length:99
                                   438       448       458       468       478       488       498       508       518         
           GRB7_HUMAN   429 QLWFHGRISREESQRLIGQQGLVDGLFLVRESQRNPQGFVLSLCHLQKVKHYLILPSEEEGRLYFSMDDGQTRFTDLLQLVEFHQLNRGILPCLLRHCC 527
               SCOP domains d3pqzd_ D: Growth factor receptor-bound protein 7                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.hhhhhhhhhhh......eeeeee.......eeeeee....eeeeeeeee..--..eee.........hhhhhhhhhhhh.........ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --SH2  PDB: D:431-527 UniProt: 431-527                                                              PROSITE
           Transcript 1 (1) ------------------------Exon 1.14  PDB: D:453-484       Exon 1.15c  PDB: D:485-527 (gaps)           Transcript 1 (1)
           Transcript 1 (2) Exon 1.13  PDB: D:429-453-------------------------------------------------------------------------- Transcript 1 (2)
                 3pqz D 429 QLWFHGRISREESQRLIGQQGLVDGLFLVRESQRNPQGFVLSLCHLQKVKHYLILPSEE--RLYFSMDDGQTRFTDLLQLVEFHQLNRGILPCLLRHCC 527
                                   438       448       458       468       478        |- |     498       508       518         
                                                                                    487  |                                     
                                                                                       490                                     

Chain L from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 3pqz L   1 WFEGYDNTFPc  11
                                    10|
                                     11-CCS

Chain M from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 3pqz M   1 WFEGYDNTFPc  11
                                    10|
                                     11-CCS

   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, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PQZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3PQZ)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (GRB7_HUMAN | Q14451)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0005070    SH3/SH2 adaptor activity    Interacting selectively and non-covalently and simultaneously with one or more signal transduction molecules, usually acting as a scaffold to bring these molecules into close proximity either using their own SH2/SH3 domains (e.g. Grb2) or those of their target molecules (e.g. SAM68).
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0035091    phosphatidylinositol binding    Interacting selectively and non-covalently with any inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
    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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
biological process
    GO:0038128    ERBB2 signaling pathway    A series of molecular signals initiated by binding of a ligand to a member of the ERBB family of receptors on the surface of a cell, where the signal is transmitted by ERBB2. The pathway ends with regulation of a downstream cellular process, e.g. transcription. ERBB2 receptors are themselves unable to bind to ligands, but act as a signal-amplifying tyrosine kinase within a heterodimeric pair.
    GO:0007173    epidermal growth factor receptor signaling pathway    A series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor EGFR (ERBB1) on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0009967    positive regulation of signal transduction    Any process that activates or increases the frequency, rate or extent of signal transduction.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0034063    stress granule assembly    The aggregation, arrangement and bonding together of proteins and RNA molecules to form a stress granule.
cellular component
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0010494    cytoplasmic stress granule    A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GRB7_HUMAN | Q144511mw4 1wgr 2l4k 2qms 4wwq 4x6s 5d0j 5eel 5eeq

(-) Related Entries Specified in the PDB File

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