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- PDB-6hak: Crystal structure of HIV-1 reverse transcriptase (RT) in complex ... -

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Basic information

Entry
Database: PDB / ID: 6hak
TitleCrystal structure of HIV-1 reverse transcriptase (RT) in complex with a double stranded RNA represents the RT transcription initiation complex prior to nucleotide incorporation
Components
  • (Gag-Pol polyprotein) x 2
  • RNA (5'-R(P*AP*GP*UP*GP*GP*CP*GP*GP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*C)-3')
  • RNA (5'-R(P*UP*CP*CP*CP*UP*GP*UP*UP*CP*GP*GP*CP*CP*GP*CP*CP*A)-3')
KeywordsTRANSCRIPTION / tRNA-Lys3 / Protein-RNA cross-link / transcription initiation / viral RNA / DNA polymerase
Function / homology
Function and homology information


HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
sucrose / RNA / RNA (> 10) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 BH10
Human immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.95 Å
AuthorsDas, K. / Martinez, S.E. / Arnold, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37 AI027690 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Structure of HIV-1 RT/dsRNA initiation complex prior to nucleotide incorporation.
Authors: Das, K. / Martinez, S.E. / DeStefano, J.J. / Arnold, E.
History
DepositionAug 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / refine / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _refine.pdbx_diffrn_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 30, 2022Group: Author supporting evidence / Database references / Structure summary
Category: chem_comp / database_2 / pdbx_audit_support
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 2.2Jan 17, 2024Group: 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

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Assembly

Deposited unit
A: Gag-Pol polyprotein
B: Gag-Pol polyprotein
T: RNA (5'-R(P*AP*GP*UP*GP*GP*CP*GP*GP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*C)-3')
P: RNA (5'-R(P*UP*CP*CP*CP*UP*GP*UP*UP*CP*GP*GP*CP*CP*GP*CP*CP*A)-3')
C: Gag-Pol polyprotein
D: Gag-Pol polyprotein
E: RNA (5'-R(P*AP*GP*UP*GP*GP*CP*GP*GP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*C)-3')
F: RNA (5'-R(P*UP*CP*CP*CP*UP*GP*UP*UP*CP*GP*GP*CP*CP*GP*CP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,97010
Polymers257,6048
Non-polymers3672
Water181
1
A: Gag-Pol polyprotein
B: Gag-Pol polyprotein
T: RNA (5'-R(P*AP*GP*UP*GP*GP*CP*GP*GP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*C)-3')
P: RNA (5'-R(P*UP*CP*CP*CP*UP*GP*UP*UP*CP*GP*GP*CP*CP*GP*CP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,1686
Polymers128,8024
Non-polymers3672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11240 Å2
ΔGint-69 kcal/mol
Surface area50560 Å2
MethodPISA
2
C: Gag-Pol polyprotein
D: Gag-Pol polyprotein
E: RNA (5'-R(P*AP*GP*UP*GP*GP*CP*GP*GP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*C)-3')
F: RNA (5'-R(P*UP*CP*CP*CP*UP*GP*UP*UP*CP*GP*GP*CP*CP*GP*CP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)128,8024
Polymers128,8024
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10610 Å2
ΔGint-67 kcal/mol
Surface area50590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.240, 175.240, 225.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Gag-Pol polyprotein / Pr160Gag-Pol


Mass: 64022.414 Da / Num. of mol.: 2 / Mutation: Q258C, C280S, D498N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 BH10
Gene: gag-pol / Production host: Escherichia coli (E. coli)
References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus- ...References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds
#2: Protein Gag-Pol polyprotein / Pr160Gag-Pol


Mass: 51928.629 Da / Num. of mol.: 2 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 BH10
Gene: gag-pol / Production host: Escherichia coli (E. coli)
References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus- ...References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds

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RNA chain , 2 types, 4 molecules TEPF

#3: RNA chain RNA (5'-R(P*AP*GP*UP*GP*GP*CP*GP*GP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*C)-3')


Mass: 7519.592 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: pbs SEQUENCE / Source: (synth.) Human immunodeficiency virus 1
#4: RNA chain RNA (5'-R(P*UP*CP*CP*CP*UP*GP*UP*UP*CP*GP*GP*CP*CP*GP*CP*CP*A)-3')


Mass: 5331.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: tRNA(LYS3) / Source: (synth.) Homo sapiens (human)

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Sugars , 1 types, 1 molecules

#5: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 2 types, 2 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.39 Å3/Da / Density % sol: 63.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: PEG 8000, AMMONIUM SULFATE, MGCL2, GLYCEROL, SUCROSE
PH range: 6.8 - 7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 3.95→87.62 Å / Num. obs: 31549 / % possible obs: 99.9 % / Redundancy: 10.8 % / Biso Wilson estimate: 159.27 Å2 / Rmerge(I) obs: 0.236 / Net I/σ(I): 6.7
Reflection shellResolution: 3.95→4.16 Å / Redundancy: 10.1 % / Rmerge(I) obs: 2.446 / Mean I/σ(I) obs: 0.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TXL

5txl


Resolution: 3.95→87.62 Å / SU ML: 1.02 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 45.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.329 1504 4.78 %
Rwork0.293 --
obs0.296 31441 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.95→87.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15644 1582 24 1 17251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00617854
X-RAY DIFFRACTIONf_angle_d0.98724624
X-RAY DIFFRACTIONf_dihedral_angle_d15.19610585
X-RAY DIFFRACTIONf_chiral_restr0.0552762
X-RAY DIFFRACTIONf_plane_restr0.0072832
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9501-4.07760.43381370.42082691X-RAY DIFFRACTION100
4.0776-4.22330.39831250.41052667X-RAY DIFFRACTION100
4.2233-4.39240.39511370.38912683X-RAY DIFFRACTION100
4.3924-4.59230.43531250.37082683X-RAY DIFFRACTION100
4.5923-4.83440.42471140.35362703X-RAY DIFFRACTION100
4.8344-5.13720.38861420.30622698X-RAY DIFFRACTION100
5.1372-5.53380.34461480.30242686X-RAY DIFFRACTION100
5.5338-6.09060.38061370.3112735X-RAY DIFFRACTION100
6.0906-6.97160.35651470.28642735X-RAY DIFFRACTION100
6.9716-8.78220.29721460.25872775X-RAY DIFFRACTION100
8.7822-87.64150.26241460.23912881X-RAY DIFFRACTION98

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