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- PDB-5f7t: TRIM5 B-box2 and coiled-coil chimera -

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Basic information

Entry
Database: PDB / ID: 5f7t
TitleTRIM5 B-box2 and coiled-coil chimera
ComponentsTripartite motif-containing protein 5,Serine--tRNA ligase,Tripartite motif-containing protein 5
KeywordsLIGASE / tripartite motif / HIV / viral restriction / TRIM / E3 ligase / self-assembly
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 / Resolution: 2.292 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
DepositionDec 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

Downloads & links

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Assembly

Deposited unit
E: Tripartite motif-containing protein 5,Serine--tRNA ligase,Tripartite motif-containing protein 5
F: Tripartite motif-containing protein 5,Serine--tRNA ligase,Tripartite motif-containing protein 5
H: Tripartite motif-containing protein 5,Serine--tRNA ligase,Tripartite motif-containing protein 5
L: Tripartite motif-containing protein 5,Serine--tRNA ligase,Tripartite motif-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,42312
Polymers65,9004
Non-polymers5238
Water93752
1
E: Tripartite motif-containing protein 5,Serine--tRNA ligase,Tripartite motif-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6063
Polymers16,4751
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
F: Tripartite motif-containing protein 5,Serine--tRNA ligase,Tripartite motif-containing protein 5
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
H: Tripartite motif-containing protein 5,Serine--tRNA ligase,Tripartite motif-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6063
Polymers16,4751
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
L: Tripartite motif-containing protein 5,Serine--tRNA ligase,Tripartite motif-containing protein 5
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)45.802, 52.329, 69.691
Angle α, β, γ (deg.)94.770, 105.540, 103.020
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain E
21chain F
31chain H
41chain L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1LEULEUchain EEA95 - 2287 - 140
2METMETchain FFB95 - 2267 - 138
3THRTHRchain HHC95 - 2277 - 139
4THRTHRchain LLD95 - 2277 - 139

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Components

#1: Protein
Tripartite motif-containing protein 5,Serine--tRNA ligase,Tripartite motif-containing protein 5 / TRIM5alpha / Seryl-tRNA synthetase / SerRS


Mass: 16474.908 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: His-SUMO tagged
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), serine-tRNA ligase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M NaAcetate 4.6, 0.2M CaAcetate, 23% PEG 3350 / PH range: 4.6

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Data collection

DiffractionMean temperature: 100 K
Ambient temp details: 25% Ethylene glycol supplement in cryo
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.292→50 Å / Num. obs: 25190 / % possible obs: 93.9 % / Redundancy: 1.9 % / Biso Wilson estimate: 36.02 Å2 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.068 / Rrim(I) all: 0.096 / Χ2: 1.044 / Net I/av σ(I): 9.391 / Net I/σ(I): 9.4 / Num. measured all: 48380
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.381.70.16421530.9510.1640.2321.03480
2.38-2.481.80.14822520.9490.1480.211.10384.2
2.48-2.591.80.14524280.9570.1450.2051.10890.1
2.59-2.731.90.14525520.9570.1450.2041.19495.8
2.73-2.920.13326510.9590.1330.1880.97298
2.9-3.1220.10426030.9690.1040.1471.1198.2
3.12-3.4420.07926490.980.0790.1111.01398.3
3.44-3.9320.06126230.9860.0610.0871.01298.3
3.93-4.9520.05926500.9840.0590.0841.00498.1
4.95-5020.05226290.9890.0520.0730.93898.2

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.292→35.052 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2564 1301 5.17 %
Rwork0.2237 23855 -
obs0.2254 25156 93.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 306.4 Å2 / Biso mean: 64.9025 Å2 / Biso min: 25.23 Å2
Refinement stepCycle: final / Resolution: 2.292→35.052 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4289 0 8 52 4349
Biso mean--46.43 53.08 -
Num. residues----532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044381
X-RAY DIFFRACTIONf_angle_d0.7245830
X-RAY DIFFRACTIONf_chiral_restr0.029632
X-RAY DIFFRACTIONf_plane_restr0.002773
X-RAY DIFFRACTIONf_dihedral_angle_d14.2171708
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11E3259X-RAY DIFFRACTION11.36TORSIONAL
12F3259X-RAY DIFFRACTION11.36TORSIONAL
13H3259X-RAY DIFFRACTION11.36TORSIONAL
14L3259X-RAY DIFFRACTION11.36TORSIONAL
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 (%)
2.2922-2.3840.30891130.2622171228476
2.384-2.49250.27961310.25422411254285
2.4925-2.62380.30421500.25792599274992
2.6238-2.78820.30251410.26942772291397
2.7882-3.00330.31311430.27732773291698
3.0033-3.30540.3391440.26412805294998
3.3054-3.78320.25831600.21852787294798
3.7832-4.76450.22221690.1952756292598
4.7645-35.05660.20621500.18662781293198
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)
12.612-0.68430.93963.31990.33834.146-0.1-0.165-0.2495-0.0804-0.02730.07350.0536-0.15150.08510.5169-0.011-0.0110.3741-0.03740.4922-7.4239-5.3065-10.7195
23.9845-0.49493.68030.7878-1.06363.5571-0.1328-0.24470.59930.2414-0.2688-0.1791-0.0989-0.020.31660.33910.0147-0.0390.4531-0.02270.317910.19548.278415.2915
34.5233-0.18133.41241.4957-0.94876.1110.781-0.4674-0.60580.1866-0.2474-0.12631.32790.0173-0.13180.5151-0.0429-0.03540.42320.06110.344115.83910.651716.6286
42.5662-0.55620.79562.7575-0.86047.90810.3401-0.1465-0.17890.5262-0.1921-0.06070.3320.5343-0.69680.3992-0.07670.03660.38770.02520.38051.6440.42513.92
53.6671-2.82011.28953.28290.60484.47190.26070.42140.2689-0.3265-0.1586-0.42840.0730.4686-0.05610.39820.02860.01140.3320.01410.4366-11.054425.4926-14.2547
64.86592.65554.09581.61521.89863.34750.13930.33470.10180.10340.0198-0.00280.11710.266-0.05950.2703-0.03370.05960.3763-0.04950.342114.216526.82366.8057
77.03410.22781.1014.71421.9036.2310.55750.6380.77380.11050.1386-0.0215-1.2371.13390.32450.4534-0.1895-0.13990.80660.32010.65728.358928.4012-4.4464
83.84711.16292.41825.8867-0.39673.73630.02930.5529-0.0892-0.76710.3648-1.355-0.20730.4648-0.00220.71950.0462-0.04250.3365-0.06440.5317-12.45040.1521-26.775
94.86011.03570.883.85450.33152.7477-0.1763-0.54320.6450.02740.02970.69360.1199-0.3465-0.07020.53550.0207-0.07260.43040.01650.4497-20.7667-3.5364-21.4439
102.04931.1097-1.54690.6937-1.42095.2914-0.10460.65220.14280.00270.90660.4573-0.179-0.22920.20950.43440.02310.02920.3512-0.00390.4951-22.86060.59-14.8478
114.0235-0.25214.32010.37770.01294.25351.1699-0.4903-0.53090.2593-0.3514-0.1711.1557-0.3913-0.48790.4155-0.0418-0.10570.44140.03670.4846-38.7965-17.1596-37.649
126.2693-1.31432.43881.1193-0.86942.469-0.3172-0.14431.19510.3096-0.1834-0.1396-0.2597-0.09360.3760.22750.03270.01070.3068-0.03220.3495-47.1296-9.5416-44.572
134.4098-1.4653-0.70973.5921-0.85482.30610.69990.2963-0.4866-0.0408-0.40210.0911-0.3928-0.2222-0.14210.48480.0054-0.03880.4572-0.01130.4334-31.2178-10.0165-31.9559
144.3747-0.27913.04464.9886-1.08014.5320.25360.57520.0793-0.5376-0.23520.11990.14310.3432-0.02350.55320.0717-0.03060.4334-0.00250.4151-20.339218.4788-24.8497
153.34171.19583.07831.53931.78952.6202-0.15430.62520.156-0.01570.01050.14930.02620.41660.0820.4135-0.0137-0.02950.53160.04480.4154-41.056818.0238-48.0278
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'E' and (resid 95 through 136 )E0
2X-RAY DIFFRACTION2chain 'E' and (resid 137 through 171 )E0
3X-RAY DIFFRACTION3chain 'E' and (resid 172 through 206 )E0
4X-RAY DIFFRACTION4chain 'E' and (resid 207 through 228 )E0
5X-RAY DIFFRACTION5chain 'F' and (resid 95 through 136 )F0
6X-RAY DIFFRACTION6chain 'F' and (resid 137 through 215 )F0
7X-RAY DIFFRACTION7chain 'F' and (resid 216 through 226 )F0
8X-RAY DIFFRACTION8chain 'H' and (resid 95 through 105 )H0
9X-RAY DIFFRACTION9chain 'H' and (resid 106 through 120 )H0
10X-RAY DIFFRACTION10chain 'H' and (resid 121 through 129 )H0
11X-RAY DIFFRACTION11chain 'H' and (resid 130 through 171 )H0
12X-RAY DIFFRACTION12chain 'H' and (resid 172 through 205 )H0
13X-RAY DIFFRACTION13chain 'H' and (resid 206 through 227 )H0
14X-RAY DIFFRACTION14chain 'L' and (resid 95 through 136 )L0
15X-RAY DIFFRACTION15chain 'L' and (resid 137 through 227 )L0

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