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- PDB-5iea: TRIM5 B-box2 and coiled-coil chimera -

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Basic information

Entry
Database: PDB / ID: 5iea
TitleTRIM5 B-box2 and coiled-coil chimera
ComponentsTripartite motif-containing protein 5, Serine--tRNA ligase Chimera
KeywordsLIGASE / tripartite motif / HIV / viral restriction / TRIM / E3 ligase / self-assembly
Function / homology
Function and homology information


regulation of viral entry into host cell / selenocysteine biosynthetic process / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / regulation of lipopolysaccharide-mediated signaling pathway / suppression of viral release by host / serine binding / negative regulation of viral entry into host cell / negative regulation of viral transcription ...regulation of viral entry into host cell / selenocysteine biosynthetic process / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / regulation of lipopolysaccharide-mediated signaling pathway / suppression of viral release by host / serine binding / 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 / protein polyubiquitination / ubiquitin-protein transferase activity / regulation of protein localization / ubiquitin protein ligase activity / positive regulation of DNA-binding transcription factor activity / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / tRNA binding / positive regulation of MAPK cascade / innate immune response / protein kinase binding / protein homodimerization activity / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / cytosol / cytoplasm
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: 3.258 Å
AuthorsWagner, J.M. / Doss, G. / Pornillos, O.
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
DepositionFeb 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tripartite motif-containing protein 5, Serine--tRNA ligase Chimera
B: Tripartite motif-containing protein 5, Serine--tRNA ligase Chimera
C: Tripartite motif-containing protein 5, Serine--tRNA ligase Chimera
D: Tripartite motif-containing protein 5, Serine--tRNA ligase Chimera
F: Tripartite motif-containing protein 5, Serine--tRNA ligase Chimera
K: Tripartite motif-containing protein 5, Serine--tRNA ligase Chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,63418
Polymers98,8496
Non-polymers78512
Water0
1
A: Tripartite motif-containing protein 5, Serine--tRNA ligase Chimera
B: Tripartite motif-containing protein 5, Serine--tRNA ligase Chimera
D: Tripartite motif-containing protein 5, Serine--tRNA ligase Chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8179
Polymers49,4253
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Tripartite motif-containing protein 5, Serine--tRNA ligase Chimera
F: Tripartite motif-containing protein 5, Serine--tRNA ligase Chimera
K: Tripartite motif-containing protein 5, Serine--tRNA ligase Chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8179
Polymers49,4253
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.227, 71.486, 213.834
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Tripartite motif-containing protein 5, Serine--tRNA ligase Chimera / TRIM5alpha / Seryl-tRNA synthetase / SerRS / Seryl-tRNA(Ser/Sec) synthetase


Mass: 16474.908 Da / Num. of mol.: 6
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 / 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), serine-tRNA ligase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / 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: 2.75 Å3/Da / Density % sol: 55.33 %
Crystal growTemperature: 310 K / Method: vapor diffusion / pH: 6.6 / Details: 0.1 M HEPES pH 6.6 0.25 M NaCl 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 17768 / % possible obs: 100 % / Redundancy: 13.6 % / Biso Wilson estimate: 35.1 Å2 / Rsym value: 0.08 / Net I/σ(I): 26.8
Reflection shellResolution: 3.25→3.37 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.258→36.7 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3042 1431 9.68 %Thin shell
Rwork0.2602 ---
obs0.2645 14789 83.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.258→36.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5040 0 12 0 5052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055148
X-RAY DIFFRACTIONf_angle_d0.3756888
X-RAY DIFFRACTIONf_dihedral_angle_d12.2013048
X-RAY DIFFRACTIONf_chiral_restr0.028822
X-RAY DIFFRACTIONf_plane_restr0.002888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2583-3.37470.3941300.2958181X-RAY DIFFRACTION12
3.3747-3.50970.4025760.2939661X-RAY DIFFRACTION43
3.5097-3.66930.28881490.28961216X-RAY DIFFRACTION78
3.6693-3.86260.30681520.25811545X-RAY DIFFRACTION97
3.8626-4.10430.31511530.25551601X-RAY DIFFRACTION100
4.1043-4.42070.30171560.23121623X-RAY DIFFRACTION100
4.4207-4.86460.30432170.22511539X-RAY DIFFRACTION100
4.8646-5.56640.29671470.25851649X-RAY DIFFRACTION100
5.5664-7.00510.31481430.29151662X-RAY DIFFRACTION100
7.0051-36.70280.27822080.27031681X-RAY DIFFRACTION99
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)
10.7516-0.64420.01270.5286-0.10520.24920.22810.3767-0.0815-0.6035-0.41860.77330.42450.1166-0.51490.85730.2339-0.06380.106-0.24280.492732.8101-17.187313.6907
20.59740.0368-0.2281.3479-0.80622.2309-0.1822-0.01170.23810.28410.17670.3774-0.6926-0.07140.0584-0.0635-0.0151-0.01730.8785-0.21980.5546.569919.063435.7065
30.4919-0.59160.17730.8930.03830.2743-0.4768-0.6273-0.69430.48190.07930.0702-0.0581-0.2562-0.6283-0.00340.21320.28040.97150.00370.49060.663114.992439.7722
40.3551-0.0053-0.22540.219-0.21320.34690.0153-0.1666-0.57870.24730.08720.25490.0309-0.42290.43480.74510.29070.58961.17840.31190.432810.9415-3.745850.3042
50.8751-0.02140.630.57770.1632.54040.17380.2151-0.2746-0.0029-0.1396-0.27510.27070.7463-0.04110.73690.08050.20970.07680.00380.491136.832928.828417.7366
60.3491-0.19390.14420.25370.09240.36040.21010.2775-0.3924-0.0981-0.10010.5630.5175-0.0380.54741.09980.2927-0.3560.7297-0.63570.470514.0949-6.89963.1947
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain F
6X-RAY DIFFRACTION6chain K

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