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- PDB-5eiu: Mini TRIM5 B-box 2 dimer C2 crystal form -

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Basic information

Entry
Database: PDB / ID: 5eiu
TitleMini TRIM5 B-box 2 dimer C2 crystal form
ComponentsTRIM protein-E3 ligase Chimera
KeywordsLIGASE / tripartite motif / HIV / viral restriction / TRIM protein / E3 ligase / self-assembly / pattern recognition
Function / homology
Function and homology information


selenocysteine biosynthetic process / regulation of viral entry into host cell / seryl-tRNA aminoacylation / serine-tRNA ligase / serine-tRNA ligase activity / regulation of lipopolysaccharide-mediated signaling pathway / suppression of viral release by host / negative regulation of viral entry into host cell / serine binding / negative regulation of viral transcription ...selenocysteine biosynthetic process / regulation of viral entry into host cell / seryl-tRNA aminoacylation / serine-tRNA ligase / serine-tRNA ligase activity / regulation of lipopolysaccharide-mediated signaling pathway / suppression of viral release by host / negative regulation of viral entry into host cell / serine binding / 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 / tRNA binding / innate immune response / protein kinase binding / protein homodimerization activity / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Serine-tRNA synthetase, type1, N-terminal / Seryl-tRNA synthetase N-terminal domain / Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Butyrophylin-like, SPRY domain / B-box zinc finger ...Serine-tRNA synthetase, type1, N-terminal / Seryl-tRNA synthetase N-terminal domain / Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / 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. / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / 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
Similarity search - Domain/homology
Serine--tRNA ligase / Tripartite motif-containing protein 5
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Thermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.908 Å
AuthorsWagner, J.M. / Doss, G. / Pornillos, O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM112508-02 United States
CitationJournal: Elife / Year: 2016
Title: Mechanism of B-box 2 domain-mediated higher-order assembly of the retroviral restriction factor TRIM5 alpha.
Authors: Wagner, J.M. / Roganowicz, M.D. / Skorupka, K. / Alam, S.L. / Christensen, D.E. / Doss, G.L. / Wan, Y. / Frank, G.A. / Ganser-Pornillos, B.K. / Sundquist, W.I. / Pornillos, O.
History
DepositionOct 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRIM protein-E3 ligase Chimera
D: TRIM protein-E3 ligase Chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2116
Polymers32,9502
Non-polymers2624
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-1 kcal/mol
Surface area16310 Å2
2
A: TRIM protein-E3 ligase Chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6063
Polymers16,4751
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
D: TRIM protein-E3 ligase Chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6063
Polymers16,4751
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.662, 41.488, 111.301
Angle α, β, γ (deg.)90.000, 99.060, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: HOH / End label comp-ID: HOH / Auth seq-ID: 95 - 801 / Label seq-ID: 7

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA - G
2chain DDB - H

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Components

#1: Protein TRIM protein-E3 ligase Chimera / TRIM5alpha / Seryl-tRNA synthetase / SerRS / Seryl-tRNA(Ser/Sec) synthetase


Mass: 16474.908 Da / Num. of mol.: 2 / Fragment: TRIM5 B-box 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey), (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Gene: TRIM5, serS, TT_C0520 / Plasmid: pET30a / Strain: HB27 / ATCC BAA-163 / DSM 7039 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q0PF16, UniProt: P34945, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.51 Å3/Da / Density % sol: 51.07 % / Description: Thick rectangular plates
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Tris 7.0, 0.2M NaCl, 28% PEG3350, + (0.025% w/v Ala-ala, 0.025% w/v Ala-gly, 0.025% w/v Gly-gly-gly-gly, 0.025% w/v Leu-gly-gly from silver bullet)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 25826 / % possible obs: 98.6 % / Redundancy: 3.5 % / Net I/σ(I): 14
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.115 / Mean I/σ(I) obs: 1.2 / % possible all: 90.4

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Processing

Software
NameVersionClassification
SERGUIdata collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.908→32.475 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2171 1254 4.96 %Random selection
Rwork0.1829 24046 --
obs0.1846 25300 98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 193.15 Å2 / Biso mean: 69.3148 Å2 / Biso min: 27.27 Å2
Refinement stepCycle: final / Resolution: 1.908→32.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2137 0 4 99 2240
Biso mean--36.6 53.34 -
Num. residues----266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192210
X-RAY DIFFRACTIONf_angle_d1.6442945
X-RAY DIFFRACTIONf_chiral_restr0.074319
X-RAY DIFFRACTIONf_plane_restr0.008391
X-RAY DIFFRACTIONf_dihedral_angle_d14.615869
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1542X-RAY DIFFRACTION7.531TORSIONAL
12D1542X-RAY DIFFRACTION7.531TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.908-1.98430.311170.29672301241885
1.9843-2.07460.30921490.25082643279298
2.0746-2.1840.22191230.218227172840100
2.184-2.32080.24611530.200127182871100
2.3208-2.49990.23831260.198426852811100
2.4999-2.75140.23471540.207127162870100
2.7514-3.14920.28851420.21227322874100
3.1492-3.96660.23271300.173627452875100
3.9666-32.47970.16421600.15242789294999
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)
11.7742-2.0098-0.46562.5773-0.18454.9790.31730.24430.1971-0.0693-0.0962-0.1837-0.5768-0.09740.00010.36060.0809-0.0030.37590.04040.401-3.125-18.0041-57.4926
21.3722-0.9667-0.13722.86160.9491.4738-0.5134-0.1093-0.31930.65630.06410.47630.9315-0.65020.00190.4494-0.05710.0240.4480.0020.4602-14.8736-26.0888-31.2715
32.9488-0.9274-2.48081.42550.33273.2984-0.0122-0.05640.11240.37520.09460.0713-0.0955-0.66490.00020.45680.0875-0.01810.5334-0.00130.4282-18.0226-18.0588-29.6667
40.67220.078-0.61580.61410.15721.6179-0.05290.465-0.7013-0.1679-0.20630.98691.1658-0.7382-0.0310.3455-0.0515-0.06750.5419-0.0580.5412-3.1692-29.0454-71.8772
52.6566-0.5047-1.13260.12780.28830.66450.0872-0.3214-0.28050.0392-0.1696-0.04340.30340.089500.3603-0.0247-0.04140.3417-0.04870.43547.9059-27.7175-68.4264
61.3999-0.1859-0.09211.88290.57831.1180.86511.00910.7504-0.82020.13-0.2857-1.7789-0.38480.00710.9586-0.04060.19660.7840.04650.605419.9615-17.1623-95.0482
70.55160.65530.75422.5925-0.88782.6669-0.13791.7606-0.1119-0.57410.1464-0.48730.0936-1.0576-0.03110.7133-0.04760.05360.9387-0.11220.573319.1794-24.6918-97.5865
80.55540.13890.21950.54440.14240.99240.2502-1.0393-0.5120.6715-0.2883-0.6252-0.77311.8730.01130.4314-0.08640.00580.6016-0.02810.527419.8121-25.0439-86.124
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 95 through 129 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 130 through 169 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 170 through 228 )A0
4X-RAY DIFFRACTION4chain 'D' and (resid 95 through 105 )D0
5X-RAY DIFFRACTION5chain 'D' and (resid 106 through 129 )D0
6X-RAY DIFFRACTION6chain 'D' and (resid 130 through 173 )D0
7X-RAY DIFFRACTION7chain 'D' and (resid 174 through 215 )D0
8X-RAY DIFFRACTION8chain 'D' and (resid 216 through 226 )D0

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