[English] 日本語
Yorodumi
- PDB-5k3q: Rhesus macaques Trim5alpha Bbox2 domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5k3q
TitleRhesus macaques Trim5alpha Bbox2 domain
ComponentsTripartite motif-containing protein 5,Tripartite motif-containing protein 5
KeywordsLIGASE / Zinc finger Bbox2 Antiretroviral
Function / homology
Function and homology information


regulation of viral entry into host cell / regulation of lipopolysaccharide-mediated signaling pathway / suppression of viral release by host / negative regulation of viral entry into host cell / negative regulation of viral transcription / pattern recognition receptor activity / negative regulation of viral genome replication / protein K63-linked ubiquitination / positive regulation of autophagy / activation of innate immune response ...regulation of viral entry into host cell / regulation of lipopolysaccharide-mediated signaling pathway / suppression of viral release by host / negative regulation of viral entry into host cell / negative regulation of viral transcription / pattern recognition receptor activity / negative regulation of viral genome replication / protein K63-linked ubiquitination / positive regulation of autophagy / activation of innate immune response / P-body / RING-type E3 ubiquitin transferase / autophagy / positive regulation of DNA-binding transcription factor activity / protein polyubiquitination / ubiquitin-protein transferase activity / regulation of protein localization / ubiquitin protein ligase activity / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / positive regulation of MAPK cascade / innate immune response / protein kinase binding / protein homodimerization activity / zinc ion binding / nucleoplasm / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Classic Zinc Finger / SPRY domain / B30.2/SPRY domain ...Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Classic Zinc Finger / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Double Stranded RNA Binding Domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Tripartite motif-containing protein 5
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsKeown, J.K. / Goldstone, D.C.
Funding support New Zealand, 2items
OrganizationGrant numberCountry
Marsden Fund New Zealand
Rutherford Fellowship New Zealand
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Crystal structure of the Trim5 alpha Bbox2 domain from rhesus macaques describes a plastic oligomerisation interface.
Authors: Keown, J.R. / Goldstone, D.C.
History
DepositionMay 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Aug 24, 2016Group: Database references
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 6, 2024Group: Author supporting evidence / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tripartite motif-containing protein 5,Tripartite motif-containing protein 5
B: Tripartite motif-containing protein 5,Tripartite motif-containing protein 5
C: Tripartite motif-containing protein 5,Tripartite motif-containing protein 5
D: Tripartite motif-containing protein 5,Tripartite motif-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,57113
Polymers46,9864
Non-polymers5859
Water1,45981
1
A: Tripartite motif-containing protein 5,Tripartite motif-containing protein 5
B: Tripartite motif-containing protein 5,Tripartite motif-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8177
Polymers23,4932
Non-polymers3245
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Tripartite motif-containing protein 5,Tripartite motif-containing protein 5
D: Tripartite motif-containing protein 5,Tripartite motif-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7556
Polymers23,4932
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.751, 54.556, 54.479
Angle α, β, γ (deg.)90.000, 100.030, 90.000
Int Tables number4
Space group name H-MP1211
DetailsDimer confirmed analytical ultracentrifugation

-
Components

#1: Protein
Tripartite motif-containing protein 5,Tripartite motif-containing protein 5 / TRIM5alpha


Mass: 11746.503 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: TRIM5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q0PF16, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsWhile no protease is present, the authors are confident that the crystal is a fragment comprising ...While no protease is present, the authors are confident that the crystal is a fragment comprising residues 94-136 of the original construct.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45 % / Description: 100 micron rectangular plate
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 24% (w/v) PE3350, 0.4 M LiNO3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 25, 2016
RadiationMonochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→38.25 Å / Num. obs: 16550 / % possible obs: 100 % / Redundancy: 7.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Net I/σ(I): 17.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.8-1.847.50.9071100
9-38.256.60.052199.2

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassification
REFMACrefinement
Aimless0.5.15data scaling
SHELX2006/3phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.8→38.25 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.622 / SU ML: 0.105 / SU R Cruickshank DPI: 0.2498 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.128
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 873 5.3 %RANDOM
Rwork0.1774 ---
obs0.1801 15677 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 64.88 Å2 / Biso mean: 27.984 Å2 / Biso min: 14.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å2-1.29 Å2
2---0.77 Å2-0 Å2
3---1.32 Å2
Refinement stepCycle: final / Resolution: 1.8→38.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1357 0 12 81 1450
Biso mean--32.18 35.39 -
Num. residues----169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191410
X-RAY DIFFRACTIONr_bond_other_d0.0030.021283
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.9121895
X-RAY DIFFRACTIONr_angle_other_deg0.8732956
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8635171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57823.64974
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59815251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.405158
X-RAY DIFFRACTIONr_chiral_restr0.0630.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021582
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02352
X-RAY DIFFRACTIONr_mcbond_it2.1422.684678
X-RAY DIFFRACTIONr_mcbond_other2.1282.682677
X-RAY DIFFRACTIONr_mcangle_it2.7384.012842
X-RAY DIFFRACTIONr_rigid_bond_restr2.95232693
X-RAY DIFFRACTIONr_sphericity_free33.221535
X-RAY DIFFRACTIONr_sphericity_bonded15.16252714
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 53 -
Rwork0.209 1140 -
all-1193 -
obs--100 %

+
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://pdbjlvh1.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