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- PDB-5w9a: The structure of the Trim5alpha Bbox- coiled coil in complex LC3B -

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Basic information

Entry
Database: PDB / ID: 5w9a
TitleThe structure of the Trim5alpha Bbox- coiled coil in complex LC3B
Components
  • Microtubule-associated proteins 1A/1B light chain 3B
  • Tripartite motif-containing protein 5
KeywordsANTIVIRAL PROTEIN / Autophagy Trim5alpha LC3B Antiviral protein
Function / homology
Function and homology information


SARS-CoV-2 modulates autophagy / regulation of viral entry into host cell / regulation of lipopolysaccharide-mediated signaling pathway / suppression of viral release by host / ceramide binding / negative regulation of viral entry into host cell / negative regulation of viral transcription / cellular response to nitrogen starvation / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex ...SARS-CoV-2 modulates autophagy / regulation of viral entry into host cell / regulation of lipopolysaccharide-mediated signaling pathway / suppression of viral release by host / ceramide binding / negative regulation of viral entry into host cell / negative regulation of viral transcription / cellular response to nitrogen starvation / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / pattern recognition receptor activity / Macroautophagy / Receptor Mediated Mitophagy / negative regulation of viral genome replication / axoneme / autophagosome membrane / organelle membrane / autophagosome maturation / protein K63-linked ubiquitination / mitophagy / autophagosome assembly / autophagosome / endomembrane system / positive regulation of autophagy / PINK1-PRKN Mediated Mitophagy / Pexophagy / cellular response to starvation / activation of innate immune response / mitochondrial membrane / macroautophagy / 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 / KEAP1-NFE2L2 pathway / ubiquitin protein ligase activity / positive regulation of NF-kappaB transcription factor activity / Translation of Replicase and Assembly of the Replication Transcription Complex / cytoplasmic vesicle / microtubule binding / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / microtubule / positive regulation of MAPK cascade / intracellular membrane-bounded organelle / innate immune response / ubiquitin protein ligase binding / protein kinase binding / protein homodimerization activity / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / SPRY domain ...Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / 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. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin-like (UB roll) / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Tripartite motif-containing protein 5 / Microtubule-associated proteins 1A/1B light chain 3B
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.74 Å
AuthorsKeown, J.R. / Goldstone, D.C.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: A helical LC3-interacting region mediates the interaction between the retroviral restriction factor Trim5 alpha and mammalian autophagy-related ATG8 proteins.
Authors: Keown, J.R. / Black, M.M. / Ferron, A. / Yap, M. / Barnett, M.J. / Pearce, F.G. / Stoye, J.P. / Goldstone, D.C.
History
DepositionJun 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _entity.formula_weight
Revision 1.2Dec 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_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_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tripartite motif-containing protein 5
C: Microtubule-associated proteins 1A/1B light chain 3B
D: Microtubule-associated proteins 1A/1B light chain 3B
B: Tripartite motif-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3958
Polymers73,1344
Non-polymers2624
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, SEC-MALLS shows that the Trim5alpha is an antiparallel coiled coil dimer, light scattering, LC3B is monomeric as shown by SEC-MALLS, Sedimentation velocity analytical ...Evidence: light scattering, SEC-MALLS shows that the Trim5alpha is an antiparallel coiled coil dimer, light scattering, LC3B is monomeric as shown by SEC-MALLS, Sedimentation velocity analytical ultracentrifugation experiments have shown a 1:1 binding scheme
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.014, 115.319, 174.164
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 95 through 112 or (resid 113...
21(chain B and (resid 95 through 109 or (resid 110...
12(chain C and (resid 4 through 42 or (resid 43...
22(chain D and ((resid 4 through 5 and (name N...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPSERSER(chain A and (resid 95 through 112 or (resid 113...AA95 - 1121 - 18
121LYSLYSLYSLYS(chain A and (resid 95 through 112 or (resid 113...AA11319
131ASPASPLEULEU(chain A and (resid 95 through 112 or (resid 113...AA95 - 2871 - 193
141ASPASPLEULEU(chain A and (resid 95 through 112 or (resid 113...AA95 - 2871 - 193
151ASPASPLEULEU(chain A and (resid 95 through 112 or (resid 113...AA95 - 2871 - 193
161ASPASPLEULEU(chain A and (resid 95 through 112 or (resid 113...AA95 - 2871 - 193
211ASPASPGLNGLN(chain B and (resid 95 through 109 or (resid 110...BD95 - 1091 - 15
221GLUGLUGLUGLU(chain B and (resid 95 through 109 or (resid 110...BD11016
231ASPASPLEULEU(chain B and (resid 95 through 109 or (resid 110...BD95 - 2871 - 193
241ASPASPLEULEU(chain B and (resid 95 through 109 or (resid 110...BD95 - 2871 - 193
251ASPASPLEULEU(chain B and (resid 95 through 109 or (resid 110...BD95 - 2871 - 193
261ASPASPLEULEU(chain B and (resid 95 through 109 or (resid 110...BD95 - 2871 - 193
112GLUGLULYSLYS(chain C and (resid 4 through 42 or (resid 43...CB4 - 421 - 39
122GLNGLNGLNGLN(chain C and (resid 4 through 42 or (resid 43...CB4340
132GLUGLUGLUGLU(chain C and (resid 4 through 42 or (resid 43...CB4 - 1171 - 114
142GLUGLUGLUGLU(chain C and (resid 4 through 42 or (resid 43...CB4 - 1171 - 114
152GLUGLUGLUGLU(chain C and (resid 4 through 42 or (resid 43...CB4 - 1171 - 114
162GLUGLUGLUGLU(chain C and (resid 4 through 42 or (resid 43...CB4 - 1171 - 114
212GLUGLULYSLYS(chain D and ((resid 4 through 5 and (name N...DC4 - 51 - 2
222GLUGLUGLNGLN(chain D and ((resid 4 through 5 and (name N...DC4 - 1161 - 113
232GLUGLUGLNGLN(chain D and ((resid 4 through 5 and (name N...DC4 - 1161 - 113
242GLUGLUGLNGLN(chain D and ((resid 4 through 5 and (name N...DC4 - 1161 - 113
252GLUGLUGLNGLN(chain D and ((resid 4 through 5 and (name N...DC4 - 1161 - 113

NCS ensembles :
ID
1
2

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Components

#1: Protein Tripartite motif-containing protein 5 / RING-type E3 ubiquitin transferase TRIM5 / TRIM5alpha


Mass: 23037.248 Da / Num. of mol.: 2 / Fragment: UNP residue 88-296 / Mutation: E120K, R121D
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, RING-type E3 ubiquitin transferase
#2: Protein Microtubule-associated proteins 1A/1B light chain 3B / Autophagy-related protein LC3 B / Autophagy-related ubiquitin-like modifier LC3 B / MAP1 light ...Autophagy-related protein LC3 B / Autophagy-related ubiquitin-like modifier LC3 B / MAP1 light chain 3-like protein 2 / MAP1A/MAP1B light chain 3 B / MAP1A/MAP1B LC3 B / Microtubule-associated protein 1 light chain 3 beta


Mass: 13529.565 Da / Num. of mol.: 2 / Fragment: UNP residues 2-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3B, MAP1ALC3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GZQ8
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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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: 4.71 Å3/Da / Density % sol: 73.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M NH4Cl, 0.1 M Tris pH8, 20% PEG 6,000

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.25 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25 Å / Relative weight: 1
ReflectionResolution: 2.74→40.91 Å / Num. obs: 24308 / % possible obs: 92.9 % / Redundancy: 12.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.034 / Rrim(I) all: 0.12 / Net I/σ(I): 13 / Num. measured all: 298683
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.74-2.96913.21.821604112150.3670.5141.8921.561.7
8.961-40.9110.30.0461252812140.9980.0140.04840.198.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å48.08 Å
Translation3 Å48.08 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
PHASER2.5.7phasing
XDS3.22data reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TN3, 3WAO

4tn3

3wao


Resolution: 2.74→40.91 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2743 1214 5 %RANDOM
Rwork0.2595 23051 --
obs0.2602 24265 62.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.96 Å2 / Biso mean: 86.3081 Å2 / Biso min: 28.99 Å2
Refinement stepCycle: final / Resolution: 2.74→40.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4845 0 4 0 4849
Biso mean--95.6 --
Num. residues----611
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1776X-RAY DIFFRACTION7.59TORSIONAL
12B1776X-RAY DIFFRACTION7.59TORSIONAL
21C1091X-RAY DIFFRACTION7.59TORSIONAL
22D1091X-RAY DIFFRACTION7.59TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7396-2.84920.3321170.41973263438
2.8492-2.97890.4141480.421392397123
2.9789-3.13590.3607760.37441431150735
3.1359-3.33230.32911050.3581983208849
3.3323-3.58940.35821450.34972762290768
3.5894-3.95040.27731740.2973309348381
3.9504-4.52140.30442040.26143861406594
4.5214-5.6940.25122170.238341354352100
5.694-40.9150.23962280.22024321454999

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