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(-) Description

Title :  CRYSTAL-STRUCTURE OF THE N-TERMINAL LARGE GTPASE DOMAIN OF HUMAN GUANYLATE BINDING PROTEIN 1 (HGBP1) IN COMPLEX WITH GMP
 
Authors :  A. Ghosh, G. J. K Praefcke, L. Renault, A. Wittinghofer, C. Herrmann
Date :  19 Oct 05  (Deposition) - 07 Mar 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Protein- Guanine Nucleotide Complex, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Ghosh, G. J. Praefcke, L. Renault, A. Wittinghofer, C. Herrmann
How Guanylate-Binding Proteins Achieve Assembly-Stimulated Processive Cleavage Of Gtp To Gmp.
Nature V. 440 101 2006
PubMed-ID: 16511497  |  Reference-DOI: 10.1038/NATURE04510
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INTERFERON-INDUCED GUANYLATE-BINDING PROTEIN 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPQE9
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL LARGE GTPASE DOMAIN
    GeneGBP1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGTP-BINDING PROTEIN 1, GUANINE NUCLEOTIDE-BINDING PROTEIN 1, HUGBP-1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
15GP2Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
15GP1Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
15GP1Ligand/IonGUANOSINE-5'-MONOPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:48 , THR A:49 , GLY A:50 , LYS A:51 , SER A:52 , PHE A:65 , SER A:66 , GLY A:68 , ARG A:183 , ASP A:184 , PRO A:241 , HOH A:599 , HOH A:606BINDING SITE FOR RESIDUE 5GP A 593
2AC2SOFTWAREARG B:48 , THR B:49 , GLY B:50 , LYS B:51 , SER B:52 , PHE B:65 , SER B:66 , GLY B:68 , ILE B:131 , ARG B:183 , ASP B:184 , PRO B:241 , HOH B:598 , HOH B:640 , HOH B:649BINDING SITE FOR RESIDUE 5GP B 593

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D4H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D4H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_033950I78VGBP1_HUMANPolymorphism1048401A/BI78V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_033950I78VGBP1_HUMANPolymorphism1048401AI78V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_033950I78VGBP1_HUMANPolymorphism1048401BI78V

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_GB1_RHD3PS51715 GB1/RHD3-type guanine nucleotide-binding (G) domain profile.GBP1_HUMAN35-278
 
  2A:35-278
B:35-278
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_GB1_RHD3PS51715 GB1/RHD3-type guanine nucleotide-binding (G) domain profile.GBP1_HUMAN35-278
 
  1A:35-278
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_GB1_RHD3PS51715 GB1/RHD3-type guanine nucleotide-binding (G) domain profile.GBP1_HUMAN35-278
 
  1-
B:35-278

(-) Exons   (6, 12)

Asymmetric Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003704731aENSE00001452810chr1:89531043-89530843201GBP1_HUMAN-00--
1.2aENST000003704732aENSE00001452808chr1:89528936-89528728209GBP1_HUMAN1-64642A:5-64
B:6-64
60
59
1.5aENST000003704735aENSE00001676167chr1:89526007-89525880128GBP1_HUMAN64-106432A:64-105 (gaps)
B:64-102 (gaps)
42
39
1.6bENST000003704736bENSE00001681134chr1:89525109-89525000110GBP1_HUMAN107-143372A:109-143
B:110-143
35
34
1.6eENST000003704736eENSE00000776340chr1:89524726-89524524203GBP1_HUMAN143-211692A:143-211 (gaps)
B:143-211 (gaps)
69
69
1.7ENST000003704737ENSE00001753781chr1:89523917-89523675243GBP1_HUMAN211-292822A:211-292
B:211-292
82
82
1.8aENST000003704738aENSE00001797851chr1:89522817-89522537281GBP1_HUMAN292-385942A:292-316
B:292-311
25
20
1.9aENST000003704739aENSE00001650939chr1:89521911-89521699213GBP1_HUMAN386-456710--
1.10cENST0000037047310cENSE00001675983chr1:89520898-89520796103GBP1_HUMAN457-491350--
1.10eENST0000037047310eENSE00001654998chr1:89520558-89520365194GBP1_HUMAN491-555650--
1.11dENST0000037047311dENSE00001883245chr1:89519151-895180021150GBP1_HUMAN556-592370--

(-) 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:299
 aligned with GBP1_HUMAN | P32455 from UniProtKB/Swiss-Prot  Length:592

    Alignment length:312
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314  
           GBP1_HUMAN     5 IHMTGPMCLIENTNGRLMANPEALKILSAITQPMVVVAIVGLYRTGKSYLMNKLAGKKKGFSLGSTVQSHTKGIWMWCVPHPKKPGHILVLLDTEGLGDVEKGDNQNDSWIFALAVLLSSTFVYNSIGTINQQAMDQLYYVTELTHRIRSKSSPDENENEVEDSADFVSFFPDFVWTLRDFSLDLEADGQPLTPDEYLTYSLKLKKGTSQKDETFNLPRLCIRKFFPKKKCFVFDRPVHRRKLAQLEKLQDEELDPEFVQQVADFCSYIFSNSKTKTLSGGIQVNGPRLESLVLTYVNAISSGDLPCMENAV 316
               SCOP domains d2d4ha1 A:5-283 automated matches                                                                                                                                                                                                                                                      d2d4ha2 A:284-316                 SCOP domains
               CATH domains 2d4hA00 A:5-316 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeee..eeeehhhhhhhhhhh...eeeeeeee....hhhhhhhhhhh....ee......---.eeeeeeee.......eeeeeeee......---..hhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhhhhhhh.....-------.........eeeeeee.............hhhhhhhhhh.........hhhhhhhhhhhhhhh..eeeee..............eehhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------V---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------G_GB1_RHD3  PDB: A:35-278 UniProt: 35-278                                                                                                                                                                                                           -------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:5-64 UniProt: 1-64 [INCOMPLETE]           ------------------------------------------Exon 1.6b  PDB: A:109-143            -------------------------------------------------------------------Exon 1.7  PDB: A:211-292 UniProt: 211-292                                         ------------------------ Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------Exon 1.5a  PDB: A:64-105 (gaps)            ------------------------------------Exon 1.6e  PDB: A:143-211 (gaps) UniProt: 143-211                    --------------------------------------------------------------------------------Exon 1.8a  PDB: A:292-316 Transcript 1 (2)
                 2d4h A   5 IHMTGPMCLIENTNGRLMANPEALKILSAITQPMVVVAIVGLYRTGKSYLMNKLAGKKKGFSLGSTVQ---KGIWMWCVPHPKKPGHILVLLDTEGLGDVE---NQNDSWIFALAVLLSSTFVYNSIGTINQQAMDQLYYVTELTHRIRSKSSPDE-------SADFVSFFPDFVWTLRDFSLDLEADGQPLTPDEYLTYSLKLKKGTSQKDETFNLPRLCIRKFFPKKKCFVFDRPVHRRKLAQLEKLQDEELDPEFVQQVADFCSYIFSNSKTKTLSGGIQVNGPRLESLVLTYVNAISSGDLPCMENAV 316
                                    14        24        34        44        54        64       | - |      84        94       104|   |  114       124       134       144       154     |   -   |   174       184       194       204       214       224       234       244       254       264       274       284       294       304       314  
                                                                                              72  76                          105 109                                                160     168                                                                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:284
 aligned with GBP1_HUMAN | P32455 from UniProtKB/Swiss-Prot  Length:592

    Alignment length:306
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305      
           GBP1_HUMAN     6 HMTGPMCLIENTNGRLMANPEALKILSAITQPMVVVAIVGLYRTGKSYLMNKLAGKKKGFSLGSTVQSHTKGIWMWCVPHPKKPGHILVLLDTEGLGDVEKGDNQNDSWIFALAVLLSSTFVYNSIGTINQQAMDQLYYVTELTHRIRSKSSPDENENEVEDSADFVSFFPDFVWTLRDFSLDLEADGQPLTPDEYLTYSLKLKKGTSQKDETFNLPRLCIRKFFPKKKCFVFDRPVHRRKLAQLEKLQDEELDPEFVQQVADFCSYIFSNSKTKTLSGGIQVNGPRLESLVLTYVNAISSGDLPC 311
               SCOP domains d2d4hb1 B:6-283 automated matches                                                                                                                                                                                                                                                     d2d4hb2 B:284-311            SCOP domains
               CATH domains 2d4hB00 B:6-311 P-loop containing nucleotide triphosphate hydrol      ases                                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee......eehhhhhhhhhh....eeeeeeee....hhhhhhhhhh.....ee...------.eeeeeeee.......eeeeeeee...-------.hhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhhhhhhhh.---------..........eeeeeee.............hhhhhhhhhh......hhhhhhhhhhhhhhhhhh..eeeee..............eehhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------V----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------G_GB1_RHD3  PDB: B:35-278 UniProt: 35-278                                                                                                                                                                                                           --------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: B:6-64 UniProt: 1-64 [INCOMPLETE]          ------------------------------------------Exon 1.6b  PDB: B:110-143            -------------------------------------------------------------------Exon 1.7  PDB: B:211-292 UniProt: 211-292                                         ------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------Exon 1.5a  PDB: B:64-102 (gaps)            ------------------------------------Exon 1.6e  PDB: B:143-211 (gaps) UniProt: 143-211                    --------------------------------------------------------------------------------Exon 1.8a            Transcript 1 (2)
                 2d4h B   6 HMTGPMCLIENTNGRLMANPEALKILSAITQPMVVVAIVGLYRTGKSYLMNKLAGKKKGFSLGS------KGIWMWCVPHPKKPGHILVLLDTEGLG-------QNDSWIFALAVLLSSTFVYNSIGTINQQAMDQLYYVTELTHRIRSKSS---------DSADFVSFFPDFVWTLRDFSLDLEADGQPLTPDEYLTYSLKLKKGTSQKDETFNLPRLCIRKFFPKKKCFVFDRPVHRRKLAQLEKLQDEELDPEFVQQVADFCSYIFSNSKTKTLSGGIQVNGPRLESLVLTYVNAISSGDLPC 311
                                    15        25        35        45        55        65   |     -|       85        95      |  -    |  115       125       135       145       155 |       - |     175       185       195       205       215       225       235       245       255       265       275       285       295       305      
                                                                                          69     76                       102     110                                            157       167                                                                                                                                                

   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  (2, 4)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D4H)

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GBP1_HUMAN | P32455)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0051879    Hsp90 protein binding    Interacting selectively and non-covalently with Hsp90 proteins, any of a group of heat shock proteins around 90kDa in size.
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    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:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0030507    spectrin binding    Interacting selectively and non-covalently with spectrin, a protein that is the major constituent of the erythrocyte cytoskeletal network. It associates with band 4.1 (see band protein) and actin to form the cytoskeletal superstructure of the erythrocyte plasma membrane. It is composed of nonhomologous chains, alpha and beta, which aggregate side-to-side in an antiparallel fashion to form dimers, tetramers, and higher polymers.
biological process
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0060333    interferon-gamma-mediated signaling pathway    A series of molecular signals initiated by the binding of interferon-gamma to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far.
    GO:0070373    negative regulation of ERK1 and ERK2 cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0050860    negative regulation of T cell receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of signaling pathways initiated by the cross-linking of an antigen receptor on a T cell.
    GO:1900041    negative regulation of interleukin-2 secretion    Any process that stops, prevents or reduces the frequency, rate or extent of interleukin-2 secretion.
    GO:1903077    negative regulation of protein localization to plasma membrane    Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to plasma membrane.
    GO:1900025    negative regulation of substrate adhesion-dependent cell spreading    Any process that stops, prevents or reduces the frequency, rate or extent of substrate adhesion-dependent cell spreading.
    GO:0050848    regulation of calcium-mediated signaling    Any process that modulates the frequency, rate or extent of calcium-mediated signaling, the process in which a cell uses calcium ions to convert an extracellular signal into a response.
    GO:1903076    regulation of protein localization to plasma membrane    Any process that modulates the frequency, rate or extent of protein localization to plasma membrane.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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: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
        GBP1_HUMAN | P324551dg3 1f5n 2b8w 2b92 2bc9

(-) Related Entries Specified in the PDB File

1dg3 THE FULL LENGTH PROTEIN WITH H507Q MUTATION AND IN NUCLEOTIDE FREE STATE
1f5n THE FULL LENGTH PROTEIN WITH H507Q MUTATION AND IN COMPLEX WITH NON-HYDROLYSABLE GTP ANALOGUE GPPNHP
2b8w SAME PROTEIN (N-TERMINAL LARGE GTPASE DOMAIN) IN COMPLEX WITH GMP/ALF4
2b92 SAME PROTEIN (N-TERMINAL LARGE GTPASE DOMAIN) IN COMPLEX WITH GDP/ALF3