[English] 日本語
Yorodumi
- PDB-4hcp: crystal structure of Burkholderia pseudomallei effector protein c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hcp
Titlecrystal structure of Burkholderia pseudomallei effector protein chbp in complex with nedd8
Components
  • NEDD8
  • Putative ATP/GTP binding protein
KeywordsPROTEIN BINDING / deamidase / Alpha/Beta/Alpha fold / Deamidation / NEDD8/Ubiquitin / bacterial cytosol
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell cycle progression / protein-glutamine glutaminase activity / protein-glutamine glutaminase / regulation of proteolysis / protein neddylation / TGF-beta receptor signaling activates SMADs / anatomical structure morphogenesis / Iron uptake and transport / protein modification process / modification-dependent protein catabolic process ...symbiont-mediated perturbation of host cell cycle progression / protein-glutamine glutaminase activity / protein-glutamine glutaminase / regulation of proteolysis / protein neddylation / TGF-beta receptor signaling activates SMADs / anatomical structure morphogenesis / Iron uptake and transport / protein modification process / modification-dependent protein catabolic process / protein tag activity / UCH proteinases / protein localization / Cargo recognition for clathrin-mediated endocytosis / Neddylation / toxin activity / ubiquitin-dependent protein catabolic process / ubiquitin protein ligase binding / host cell nucleus / regulation of transcription by RNA polymerase II / proteolysis / extracellular exosome / extracellular region / nucleoplasm / nucleus / cytosol
Similarity search - Function
Protein-glutamine deamidase Cif / Cycle inhibiting factor (CIF) / Nedd8-like ubiquitin / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family ...Protein-glutamine deamidase Cif / Cycle inhibiting factor (CIF) / Nedd8-like ubiquitin / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
NEDD8 / Protein-glutamine deamidase Cif
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsYao, Q. / Shao, F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural mechanism of ubiquitin and NEDD8 deamidation catalyzed by bacterial effectors that induce macrophage-specific apoptosis.
Authors: Yao, Q. / Cui, J. / Wang, J. / Li, T. / Wan, X. / Luo, T. / Gong, Y.N. / Xu, Y. / Huang, N. / Shao, F.
History
DepositionOct 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: Putative ATP/GTP binding protein
B: NEDD8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4624
Polymers37,2742
Non-polymers1882
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-26 kcal/mol
Surface area14210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.389, 44.973, 67.303
Angle α, β, γ (deg.)90.00, 110.83, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Putative ATP/GTP binding protein


Mass: 28557.408 Da / Num. of mol.: 1 / Fragment: unp residues 78-382 / Mutation: A156C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: K96243 / Gene: BPSS1385 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q63KH5
#2: Protein NEDD8 / Neddylin / Neural precursor cell expressed developmentally down-regulated protein 8 / NEDD-8 / ...Neddylin / Neural precursor cell expressed developmentally down-regulated protein 8 / NEDD-8 / Ubiquitin-like protein Nedd8


Mass: 8716.133 Da / Num. of mol.: 1 / Fragment: unp residues 1-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15843
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.5
Details: 1.5 M ammonium sulfate and 100 mM citrate, pH 5.5, EVAPORATION, temperature 293K

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 11113 / Num. obs: 11021 / % possible obs: 90 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASESphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→19.84 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.858 / Cross valid method: THROUGHOUT / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26679 564 5.1 %RANDOM
Rwork0.19999 ---
obs0.20342 10457 89.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.474 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.52→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2524 0 11 94 2629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222573
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.091.9823471
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0745317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82224.576118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.97115478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.111518
X-RAY DIFFRACTIONr_chiral_restr0.0820.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211901
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
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_it0.821.51590
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40922565
X-RAY DIFFRACTIONr_scbond_it2.2073983
X-RAY DIFFRACTIONr_scangle_it3.6254.5906
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.52→2.584 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 44 -
Rwork0.204 769 -
obs--93.13 %

+
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