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- PDB-5va4: TRIM-Cyclophilin A B-box 2 and coiled-coil chimera -

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Basic information

Entry
Database: PDB / ID: 5va4
TitleTRIM-Cyclophilin A B-box 2 and coiled-coil chimera
ComponentsTRIM5/cyclophilin A V4 fusion protein
KeywordsLIGASE / B-box / trimer / self-assembly / zinc binding
Function / homology
Function and homology information


selenocysteine biosynthetic process / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / serine binding / peptidyl-prolyl cis-trans isomerase activity / protein folding / transferase activity / tRNA binding / protein homodimerization activity ...selenocysteine biosynthetic process / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / serine binding / peptidyl-prolyl cis-trans isomerase activity / protein folding / transferase activity / tRNA binding / protein homodimerization activity / zinc ion binding / ATP binding / identical protein binding / 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 / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. ...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 / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / 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) / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / 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 / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Serine--tRNA ligase / TRIM5/cyclophilin A V4 fusion protein
Similarity search - Component
Biological speciesAotus trivirgatus (douroucouli)
Thermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.306 Å
AuthorsWagner, J.M. / Ganser-Pornillos, B.K. / Pornillos, O.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM112508 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32-GM115007 United States
CitationJournal: J. Virol. / Year: 2018
Title: General Model for Retroviral Capsid Pattern Recognition by TRIM5 Proteins.
Authors: Wagner, J.M. / Christensen, D.E. / Bhattacharya, A. / Dawidziak, D.M. / Roganowicz, M.D. / Wan, Y. / Pumroy, R.A. / Demeler, B. / Ivanov, D.N. / Ganser-Pornillos, B.K. / Sundquist, W.I. / Pornillos, O.
History
DepositionMar 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.title / _citation.year
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: TRIM5/cyclophilin A V4 fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3364
Polymers16,1401
Non-polymers1963
Water45025
1
A: TRIM5/cyclophilin A V4 fusion protein
hetero molecules

A: TRIM5/cyclophilin A V4 fusion protein
hetero molecules

A: TRIM5/cyclophilin A V4 fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,00712
Polymers48,4193
Non-polymers5899
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation11_555y,-z,-x1
Buried area2920 Å2
ΔGint-106 kcal/mol
Surface area22440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.596, 104.596, 104.596
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein TRIM5/cyclophilin A V4 fusion protein / Seryl-tRNA synthetase / SerRS


Mass: 16139.511 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This is a chimera between TRIM5 sequence taken from TRIM-Cyclophilin A, and a bacterial tRNA synthetase sequence.
Source: (gene. exp.) Aotus trivirgatus (douroucouli), (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: serS, TT_C0520 / Production host: Escherichia coli (E. coli)
References: UniProt: Q68KK2, UniProt: P34945, serine-tRNA ligase
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.95 Å3/Da / Density % sol: 58.36 % / Description: cubes or prisms
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 17% PEG 3350, 0.4 M sodium/potassium tartrate

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: cryo stream
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 8544 / % possible obs: 99.6 % / Redundancy: 10.6 % / Rpim(I) all: 0.045 / Rsym value: 0.131 / Net I/σ(I): 12.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 8.5 % / Num. unique obs: 1281 / Rpim(I) all: 0.681 / Rsym value: 1 / % 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
Starting model: 5EIU

5eiu


Resolution: 2.306→27.954 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2874 862 10.09 %
Rwork0.2305 --
obs0.2364 8544 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.306→27.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms982 0 3 25 1010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081002
X-RAY DIFFRACTIONf_angle_d0.3751324
X-RAY DIFFRACTIONf_dihedral_angle_d13.365614
X-RAY DIFFRACTIONf_chiral_restr0.032148
X-RAY DIFFRACTIONf_plane_restr0.001173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3056-2.450.34981440.30711281X-RAY DIFFRACTION100
2.45-2.63910.33261400.30511262X-RAY DIFFRACTION100
2.6391-2.90440.33961430.29751275X-RAY DIFFRACTION100
2.9044-3.32410.35241370.28321263X-RAY DIFFRACTION100
3.3241-4.18570.25791500.23211300X-RAY DIFFRACTION100
4.1857-27.95650.27651480.20081301X-RAY DIFFRACTION98

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