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- PDB-1f5n: HUMAN GUANYLATE BINDING PROTEIN-1 IN COMPLEX WITH THE GTP ANALOGU... -

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Basic information

Entry
Database: PDB / ID: 1f5n
TitleHUMAN GUANYLATE BINDING PROTEIN-1 IN COMPLEX WITH THE GTP ANALOGUE, GMPPNP.
ComponentsINTERFERON-INDUCED GUANYLATE-BINDING PROTEIN 1
KeywordsSIGNALING PROTEIN / GBP / GTP Hydrolysis / GDP / GMP / Interferon Induced / Dynamin related / Large GTPase family. GMPPNP / GPPNHP.
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 protein localization to plasma membrane / negative regulation of T cell receptor signaling pathway ...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 protein localization to plasma membrane / negative regulation of T cell receptor signaling pathway / spectrin binding / negative regulation of interleukin-2 production / 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 / regulation of calcium-mediated signaling / G protein activity / lipopolysaccharide binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Hsp90 protein binding / cytoplasmic vesicle membrane / negative regulation of ERK1 and ERK2 cascade / cellular response to type II interferon / GDP binding / Interferon gamma signaling / actin cytoskeleton / cellular response to tumor necrosis factor / actin binding / cytoplasmic vesicle / defense response to virus / defense response to bacterium / Golgi membrane / innate immune response / GTPase activity / GTP binding / enzyme binding / Golgi apparatus / protein homodimerization activity / extracellular region / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Signaling Protein - Interferon-induced Guanylate-binding Protein 1; Chain A, domain 1 / Guanylate-binding protein, C-terminal domain / 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. ...Signaling Protein - Interferon-induced Guanylate-binding Protein 1; Chain A, domain 1 / Guanylate-binding protein, C-terminal domain / 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 / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / 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: 1.7 Å
AuthorsPrakash, B. / Renault, L. / Praefcke, G.J.K. / Herrmann, C. / Wittinghofer, A.
Citation
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.
#1: 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.K. / Renault, L. / Wittinghofer, A. / Herrmann, C.
#2: Journal: J.Mol.Biol. / Year: 1999
Title: Nucleotide-binding Characteristics of Human Guanylate-binding protein 1(hGBP1) and Identification of the Third GTP-binding Motif
Authors: Praefcke, G.J.K. / Geyer, M. / Schwemmle, M. / Kalbitzer, H.R. / Herrmann, C.
History
DepositionJun 15, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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)68,5503
Polymers68,0041
Non-polymers5472
Water7,404411
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)161.228, 42.652, 91.544
Angle α, β, γ (deg.)90.00, 100.19, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein INTERFERON-INDUCED GUANYLATE-BINDING PROTEIN 1


Mass: 68003.594 Da / Num. of mol.: 1 / Mutation: Q507H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PQE9 / Production host: Escherichia coli (E. coli) / 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.: 411 / 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: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15-20% PEG3350, 150-200mM MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-20 %PEG33501reservoir
2150-200 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.9903
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 16, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9903 Å / Relative weight: 1
ReflectionResolution: 1.7→41.19 Å / Num. all: 67508 / Num. obs: 67508 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.22 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 12.05
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.251 / % possible all: 73.6
Reflection shell
*PLUS
% possible obs: 74 % / Mean I/σ(I) obs: 3.7

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
MAR345data collection
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DG3 with some deletions

1dg3


Resolution: 1.7→41.19 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 924254.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: as implemented in CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 3366 5 %RANDOM
Rwork0.226 ---
all0.224 67507 --
obs0.226 67507 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.92 Å2 / ksol: 0.408 e/Å3
Displacement parametersBiso mean: 23.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.64 Å20 Å2-1.49 Å2
2--3.93 Å20 Å2
3----1.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.7→41.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4587 32 1 411 5031
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19.4
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it1.832
X-RAY DIFFRACTIONc_scbond_it2.192
X-RAY DIFFRACTIONc_scangle_it3.42.5
LS refinement shellResolution: 1.7→1.78 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.284 422 5 %
Rwork0.269 7960 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3GNP.PARGNP.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.68

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