[English] 日本語
Yorodumi
- PDB-2b8w: Crystal-structure of the N-terminal Large GTPase Domain of human ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2b8w
TitleCrystal-structure of the N-terminal Large GTPase Domain of human Guanylate Binding protein 1 (hGBP1) in complex with GMP/AlF4
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 / negative regulation of substrate adhesion-dependent cell spreading / protein localization to vacuole / symbiont cell surface / cytolysis in another organism / positive regulation of pyroptotic inflammatory response / vesicle membrane / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway ...GDP phosphatase activity / non-canonical inflammasome complex assembly / negative regulation of substrate adhesion-dependent cell spreading / protein localization to vacuole / symbiont cell surface / cytolysis in another organism / positive regulation of pyroptotic inflammatory response / vesicle membrane / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / spectrin binding / defense response to protozoan / cytokine binding / cellular response to interleukin-1 / negative regulation of protein localization to plasma membrane / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / regulation of protein localization to plasma membrane / regulation of calcium-mediated signaling / cytoplasmic vesicle membrane / Hsp90 protein binding / lipopolysaccharide binding / negative regulation of ERK1 and ERK2 cascade / cellular response to type II interferon / Interferon gamma signaling / cellular response to tumor necrosis factor / GDP binding / actin cytoskeleton / G protein activity / actin binding / cytoplasmic vesicle / defense response to virus / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / 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
Guanylate-binding protein, C-terminal / Guanylate-binding protein/Atlastin, C-terminal / Guanylate-binding protein, C-terminal domain / Guanylate-binding protein, C-terminal domain superfamily / Guanylate-binding protein, N-terminal / 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, C-terminal domain superfamily / Guanylate-binding protein, N-terminal / 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
GUANOSINE-5'-MONOPHOSPHATE / TETRAFLUOROALUMINATE ION / Guanylate-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 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 10, 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: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)75,1388
Polymers74,1572
Non-polymers9816
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-35 kcal/mol
Surface area23510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.617, 101.927, 54.121
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRHISHIS4AA8 - 24319 - 254
21THRTHRHISHIS4BB8 - 24319 - 254
32ARGARGGLNGLN5AA244 - 249255 - 260
42ARGARGGLNGLN5BB244 - 249255 - 260
53LEULEUSERSER4AA250 - 305261 - 316
63LEULEUSERSER4BB250 - 305261 - 316
745GP5GPMGMG1AE - C593 - 595
845GP5GPMGMG1BH - F593 - 595
DetailsThe biological assembly is the homodimer in the asymmetric unit

-
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.: 2 / Fragment: N-terminal Large GTPase domain
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.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#4: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.09 %
Crystal growTemperature: 298 K
Details: 5% PEG3350, 150 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2002
RadiationMonochromator: DIAMOND (111), LAUE GEOMETRY, 150 MICRONS THIN
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.22→30 Å / Num. obs: 41099 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 14.05 % / Biso Wilson estimate: 38 Å2 / Rsym value: 0.078 / Net I/σ(I): 20.6
Reflection shellResolution: 2.22→2.25 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 5.5 / Rsym value: 0.485 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F5N

1f5n


Resolution: 2.22→29.75 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 10.914 / SU ML: 0.133 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2758 6.6 %RANDOM
Rwork0.19 ---
obs0.193 38814 99.6 %-
all-38814 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.22 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å20 Å20 Å2
2---0.76 Å20 Å2
3---2.12 Å2
Refinement stepCycle: LAST / Resolution: 2.22→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4582 0 60 167 4809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224764
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7811.9876435
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7355574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.29724.343198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.7915859
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.5821522
X-RAY DIFFRACTIONr_chiral_restr0.0670.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.030.023480
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2420.21982
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3230.23180
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2235
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.217
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.391.52952
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.05724668
X-RAY DIFFRACTIONr_scbond_it5.0932072
X-RAY DIFFRACTIONr_scangle_it6.8144.51767
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
30tight positional0.460.05
2225medium positional0.30.5
29loose positional0.535
30tight thermal0.70.5
2225medium thermal1.482
29loose thermal4.6610
LS refinement shellResolution: 2.22→2.25 Å / Total num. of bins used: 35
RfactorNum. reflection% reflection
Rfree0.348 117 -
Rwork0.238 1619 -
obs--97.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.15780.47230.0770.76240.01570.39720.021-0.04370.0551-0.0089-0.01560.0662-0.0039-0.0473-0.00540.0370.00420.00760.0450.01470.009859.161619.96185.4232
21.35650.4523-0.040.7722-0.15070.5230.02110.01040.00870.0017-0.0223-0.0311-0.02020.02180.00130.03540.00110.00530.0306-0.00980.004188.743931.41684.4183
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 30817 - 319
2X-RAY DIFFRACTION1AG - C593 - 5951
3X-RAY DIFFRACTION2BB6 - 30917 - 320
4X-RAY DIFFRACTION2BH - D593 - 5951

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more