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- PDB-2bc9: Crystal-structure of the N-terminal large GTPase Domain of human ... -

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Basic information

Entry
Database: PDB / ID: 2bc9
TitleCrystal-structure of the N-terminal large GTPase Domain of human Guanylate Binding protein 1 (hGBP1) in complex with non-hydrolysable GTP analogue GppNHp
ComponentsInterferon-induced guanylate-binding protein 1
KeywordsSIGNALING PROTEIN / Protein- guanine nucleotide complex
Function / homology
Function and homology information


GDP phosphatase activity / non-canonical inflammasome complex assembly / protein localization to vacuole / negative regulation of substrate adhesion-dependent cell spreading / symbiont cell surface / cytolysis in another organism / positive regulation of pyroptotic inflammatory response / vesicle membrane / negative regulation of T cell receptor signaling pathway / negative regulation of interleukin-2 production ...GDP phosphatase activity / non-canonical inflammasome complex assembly / protein localization to vacuole / negative regulation of substrate adhesion-dependent cell spreading / symbiont cell surface / cytolysis in another organism / positive regulation of pyroptotic inflammatory response / vesicle membrane / negative regulation of T cell receptor signaling pathway / negative regulation of interleukin-2 production / spectrin binding / defense response to protozoan / cytokine binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / cellular response to interleukin-1 / regulation of protein localization to plasma membrane / negative regulation of protein localization to plasma membrane / regulation of calcium-mediated signaling / lipopolysaccharide binding / Hsp90 protein binding / cytoplasmic vesicle membrane / cellular response to type II interferon / G protein activity / negative regulation of ERK1 and ERK2 cascade / Interferon gamma signaling / GDP binding / actin cytoskeleton / cellular response to tumor necrosis factor / actin binding / cytoplasmic vesicle / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / defense response to virus / defense response to bacterium / Golgi membrane / innate immune response / GTPase activity / GTP binding / Golgi apparatus / enzyme binding / protein homodimerization activity / extracellular region / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Guanylate-binding protein, C-terminal / Guanylate-binding protein/Atlastin, C-terminal / Guanylate-binding protein, C-terminal domain / Guanylate-binding protein, N-terminal / Guanylate-binding protein, C-terminal domain superfamily / Guanylate-binding protein, N-terminal domain / GB1/RHD3-type guanine nucleotide-binding (G) domain / GB1/RHD3-type guanine nucleotide-binding (G) domain profile. / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold ...Guanylate-binding protein, C-terminal / Guanylate-binding protein/Atlastin, C-terminal / Guanylate-binding protein, C-terminal domain / Guanylate-binding protein, N-terminal / Guanylate-binding protein, C-terminal domain superfamily / Guanylate-binding protein, N-terminal domain / GB1/RHD3-type guanine nucleotide-binding (G) domain / GB1/RHD3-type guanine nucleotide-binding (G) domain profile. / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Guanylate-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGhosh, A. / Praefcke, G.J.K. / Renault, L. / Wittinghofer, A. / Herrmann, C.
Citation
Journal: Nature / Year: 2006
Title: How guanylate-binding proteins achieve assembly-stimulated processive cleavage of GTP to GMP.
Authors: Ghosh, A. / Praefcke, G.J. / Renault, L. / Wittinghofer, A. / Herrmann, C.
#1: Journal: Embo J. / Year: 2000
Title: Triphosphate structure of guanylate-binding protein 1 and implications for nucleotide binding and GTPase mechanism.
Authors: Prakash, B. / Renault, L. / Praefcke, G.J. / Herrmann, C. / Wittinghofer, A.
#2: Journal: Nature / Year: 2000
Title: Structure of human guanylate-binding protein 1 representing a unique class of GTP-binding proteins.
Authors: Prakash, B. / Praefcke, G.J. / Renault, L. / Herrmann, C. / Wittinghofer, A.
History
DepositionOct 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 2.0Aug 23, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interferon-induced guanylate-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6253
Polymers37,0781
Non-polymers5472
Water68538
1
A: Interferon-induced guanylate-binding protein 1
hetero molecules

A: Interferon-induced guanylate-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2506
Polymers74,1572
Non-polymers1,0934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y,-z+1/21
Unit cell
Length a, b, c (Å)54.884, 101.104, 149.261
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
DetailsOne of the subunit of homodimeric biological assembly is in the asymmetric unit

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Components

#1: Protein Interferon-induced guanylate-binding protein 1 / GTP-binding protein 1 / Guanine nucleotide-binding protein 1 / HuGBP-1


Mass: 37078.449 Da / Num. of mol.: 1 / Fragment: N-terminal Large GTPase doamin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GBP1 / Plasmid: pQE9 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P32455
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 10 % Peg 3350, 100 mM NaSCN, 40 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 10, 2002 / Details: Ge (220) Crystal
RadiationMonochromator: Diamond monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 10831 / Num. obs: 10593 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.8→2.9 Å / % possible all: 98.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 2B8W

2b8w


Resolution: 2.8→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.269 534 RANDOM
Rwork0.234 --
obs0.241 10010 -
all-10010 -
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2331 0 33 38 2402
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0082
X-RAY DIFFRACTIONc_angle_deg1.42865
LS refinement shellResolution: 2.8→2.9 Å /
RfactorNum. reflection
Rfree0.38 41
Rwork0.303 -

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