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- PDB-7mrl: Structure of HIV-1 matrix domain bound to human tRNALys3 -

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Basic information

Entry
Database: PDB / ID: 7mrl
TitleStructure of HIV-1 matrix domain bound to human tRNALys3
Components
  • HIV-1 matrix domain
  • tRNA Lys3
KeywordsVIRAL PROTEIN/RNA / HIV-1 / Gag / Matrix domain / RNA-protein interaction / tRNA / transfer RNA / ribonucleoprotein complex / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


viral process / viral nucleocapsid / host cell cytoplasm / host cell nucleus / structural molecule activity / RNA binding / cytoplasm
Similarity search - Function
Retroviral nucleocapsid Gag protein p24, N-terminal / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal
Similarity search - Domain/homology
RNA / RNA (> 10) / Gag protein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.15 Å
AuthorsBou-Nader, C. / Zhang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Cell Host Microbe / Year: 2021
Title: HIV-1 matrix-tRNA complex structure reveals basis for host control of Gag localization.
Authors: Bou-Nader, C. / Muecksch, F. / Brown, J.B. / Gordon, J.M. / York, A. / Peng, C. / Ghirlando, R. / Summers, M.F. / Bieniasz, P.D. / Zhang, J.
History
DepositionMay 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.2Aug 25, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Sep 22, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.4Jun 7, 2023Group: Derived calculations / Refinement description
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: HIV-1 matrix domain
A: tRNA Lys3
B: HIV-1 matrix domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8174
Polymers48,7923
Non-polymers241
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, 1:1 binding in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-31 kcal/mol
Surface area22770 Å2
Unit cell
Length a, b, c (Å)96.717, 108.846, 146.021
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain B
21(chain C and resid 7 through 107)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 7 - 107 / Label seq-ID: 6 - 106

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain BBC
2(chain C and resid 7 through 107)CA

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Components

#1: Protein HIV-1 matrix domain / Matrix protein p17 / Nucleocapsid protein p7


Mass: 12281.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli (E. coli) / References: UniProt: C1JB69
#2: RNA chain tRNA Lys3


Mass: 24228.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN

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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: 3.94 Å3/Da / Density % sol: 68.77 % / Description: Cubic
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM HEPES, 20% PEG500 MME, 10% PEG20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→45.1143 Å / Num. obs: 13692 / % possible obs: 99.74 % / Redundancy: 18.6 % / CC1/2: 0.998 / Net I/σ(I): 8.7
Reflection shellResolution: 3.15→3.263 Å / Mean I/σ(I) obs: 1.23 / Num. unique obs: 13657 / CC1/2: 0.576 / % possible all: 99.55

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3260refinement
MOSFLMdata reduction
xia2data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1HIW & 1FIR

1hiw

1fir


Resolution: 3.15→45.11 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2231 2578 10.03 %
Rwork0.1853 23128 -
obs0.1889 13657 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 216.93 Å2 / Biso min: 77.91 Å2
Refinement stepCycle: final / Resolution: 3.15→45.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1637 1606 1 0 3244
Biso mean--80.37 --
Num. residues----278
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B614X-RAY DIFFRACTION5.202TORSIONAL
12C614X-RAY DIFFRACTION5.202TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.15-3.21060.37561450.3649126698
3.2106-3.27610.36181430.33011249100
3.2761-3.34730.32071440.31611311100
3.3473-3.42510.34691490.30151302100
3.4251-3.51080.31851390.28091267100
3.5108-3.60570.27951340.26521276100
3.6057-3.71170.32271450.2311309100
3.7117-3.83140.22491480.21321301100
3.8314-3.96830.25141430.19371290100
3.9683-4.12710.25321400.20391277100
4.1271-4.31480.25661430.1931274100
4.3148-4.54210.23381410.16241290100
4.5421-4.82630.14441420.15131269100
4.8263-5.19850.22221450.15221306100
5.1985-5.72070.19651450.15751299100
5.7207-6.54630.1811420.16291272100
6.5463-8.23950.1811420.1561283100
8.2395-45.110.19771480.1623128799
Refinement TLS params.Method: refined / Origin x: 15.8852 Å / Origin y: 2.4711 Å / Origin z: 180.3268 Å
111213212223313233
T0.9205 Å20.0799 Å2-0.0143 Å2-1.0393 Å2-0.0873 Å2--1.0138 Å2
L0.5838 °20.6696 °20.1315 °2-1.9321 °2-0.4773 °2--0.3316 °2
S-0.1408 Å °-0.009 Å °-0.0194 Å °0.0342 Å °0.1568 Å °-0.1393 Å °-0.045 Å °0.1909 Å °-0.0119 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allC7 - 108
2X-RAY DIFFRACTION1allA1 - 75
3X-RAY DIFFRACTION1allB7 - 107
4X-RAY DIFFRACTION1allD1

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