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- PDB-3v6d: Crystal structure of HIV-1 reverse transcriptase (RT) cross-linke... -

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Basic information

Entry
Database: PDB / ID: 3v6d
TitleCrystal structure of HIV-1 reverse transcriptase (RT) cross-linked with AZT-terminated DNA
Components
  • DNA (5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(ATM))-3')
  • DNA (5'-D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3')
  • HIV-1 REVERSE TRANSCRIPTASE P51 subunit
  • HIV-1 REVERSE TRANSCRIPTASE P66 subunit
KeywordsTRANSFERASE/DNA / HIV-1 reverse transcriptase / zidovudine / RT-DNA complex / transferase-DNA complex / drug resistance mutation / AIDS / DNA recombination / DNA-directed DNA polymerase / RNAse H / hydrolase / lipoprotein / magnesium / membrane / metal-binding / multifunctional enzyme / nucleotidyltransferase / RNA-directed DNA polymerase transferase
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
DNA / DNA (> 10) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 BH10
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7048 Å
AuthorsDas, K. / Martinez, S.E. / Arnold, E.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2012
Title: HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism.
Authors: Das, K. / Martinez, S.E. / Bauman, J.D. / Arnold, E.
#1: Journal: J.Biol.Chem. / Year: 2009
Title: Structural basis for the role of the K65R mutation in HIV-1 reverse transcriptase polymerization, excision antagonism, and tenofovir resistance.
Authors: Das, K. / Bandwar, R.P. / White, K.L. / Feng, J.Y. / Sarafianos, S.G. / Tuske, S. / Tu, X. / Clark, A.D. / Boyer, P.L. / Hou, X. / Gaffney, B.L. / Jones, R.A. / Miller, M.D. / Hughes, S.H. / Arnold, E.
#2: Journal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structural basis of HIV-1 resistance to AZT by excision.
Authors: Tu, X. / Das, K. / Han, Q. / Bauman, J.D. / Clark, A.D. / Hou, X. / Frenkel, Y.V. / Gaffney, B.L. / Jones, R.A. / Boyer, P.L. / Hughes, S.H. / Sarafianos, S.G. / Arnold, E.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: High-resolution structures of HIV-1 reverse transcriptase/TMC278 complexes: strategic flexibility explains potency against resistance mutations.
Authors: Das, K. / Bauman, J.D. / Clark, A.D. / Frenkel, Y.V. / Lewi, P.J. / Shatkin, A.J. / Hughes, S.H. / Arnold, E.
#4: Journal: J.Med.Chem. / Year: 2004
Title: Roles of conformational and positional adaptability in structure-based design of TMC125-R165335 (etravirine) and related non-nucleoside reverse transcriptase inhibitors that are highly potent ...Title: Roles of conformational and positional adaptability in structure-based design of TMC125-R165335 (etravirine) and related non-nucleoside reverse transcriptase inhibitors that are highly potent and effective against wild-type and drug-resistant HIV-1 variants.
Authors: Das, K. / Clark, A.D. / Lewi, P.J. / Heeres, J. / De Jonge, M.R. / Koymans, L.M. / Vinkers, H.M. / Daeyaert, F. / Ludovici, D.W. / Kukla, M.J. / De Corte, B. / Kavash, R.W. / Ho, C.Y. / Ye, ...Authors: Das, K. / Clark, A.D. / Lewi, P.J. / Heeres, J. / De Jonge, M.R. / Koymans, L.M. / Vinkers, H.M. / Daeyaert, F. / Ludovici, D.W. / Kukla, M.J. / De Corte, B. / Kavash, R.W. / Ho, C.Y. / Ye, H. / Lichtenstein, M.A. / Andries, K. / Pauwels, R. / De Bethune, M.P. / Boyer, P.L. / Clark, P. / Hughes, S.H. / Janssen, P.A. / Arnold, E.
#5: Journal: Science / Year: 1998
Title: Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance.
Authors: Huang, H. / Chopra, R. / Verdine, G.L. / Harrison, S.C.
History
DepositionDec 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 13, 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 REVERSE TRANSCRIPTASE P66 subunit
B: HIV-1 REVERSE TRANSCRIPTASE P51 subunit
C: HIV-1 REVERSE TRANSCRIPTASE P66 subunit
D: HIV-1 REVERSE TRANSCRIPTASE P51 subunit
T: DNA (5'-D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3')
P: DNA (5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(ATM))-3')
E: DNA (5'-D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3')
F: DNA (5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(ATM))-3')


Theoretical massNumber of molelcules
Total (without water)257,9378
Polymers257,9378
Non-polymers00
Water0
1
A: HIV-1 REVERSE TRANSCRIPTASE P66 subunit
B: HIV-1 REVERSE TRANSCRIPTASE P51 subunit
T: DNA (5'-D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3')
P: DNA (5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(ATM))-3')


Theoretical massNumber of molelcules
Total (without water)128,9694
Polymers128,9694
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13330 Å2
ΔGint-50 kcal/mol
Surface area48470 Å2
MethodPISA
2
C: HIV-1 REVERSE TRANSCRIPTASE P66 subunit
D: HIV-1 REVERSE TRANSCRIPTASE P51 subunit
E: DNA (5'-D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3')
F: DNA (5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(ATM))-3')


Theoretical massNumber of molelcules
Total (without water)128,9694
Polymers128,9694
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13310 Å2
ΔGint-48 kcal/mol
Surface area48530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.4760, 133.1710, 139.9040
Angle α, β, γ (deg.)90.00, 98.6740, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HIV-1 REVERSE TRANSCRIPTASE P66 subunit


Mass: 64022.414 Da / Num. of mol.: 2 / Fragment: UNP Residues 600-1153 / Mutation: YES
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, RNA-directed DNA polymerase, DNA-directed DNA polymerase
#2: Protein HIV-1 REVERSE TRANSCRIPTASE P51 subunit


Mass: 50039.488 Da / Num. of mol.: 2 / Fragment: UNP Residues 600-1027
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, RNA-directed DNA polymerase, DNA-directed DNA polymerase
#3: DNA chain DNA (5'-D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3')


Mass: 8416.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthesized
#4: DNA chain DNA (5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(ATM))-3')


Mass: 6490.267 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthesized

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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: 3.23 Å3/Da / Density % sol: 61.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.8
Details: PEG 8000, ammonium sulfate, sucrose, glycerol, magnesium chloride, pH 6.8, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 1, 2011 / Details: MIRROR
RadiationMonochromator: Rh coated Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 86184 / % possible obs: 98.4 % / Observed criterion σ(I): -1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.089 / Χ2: 1.569 / Net I/σ(I): 11.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.753.20.62542111.107197.2
2.75-2.83.30.5542151.144196.7
2.8-2.853.40.49642741.186197.6
2.85-2.913.40.43942571.179197.9
2.91-2.973.50.38342691.225197.7
2.97-3.043.50.34542751.333198.4
3.04-3.123.70.28943011.376198.4
3.12-3.23.70.24243171.479198.9
3.2-3.33.90.19743391.546198.9
3.3-3.440.16443511.642199.2
3.4-3.524.10.13742931.682199.3
3.52-3.664.10.11843441.835199.2
3.66-3.834.20.10343671.786199.5
3.83-4.034.20.0943771.874199.7
4.03-4.294.30.08143421.903199.6
4.29-4.624.30.07343671.895199.6
4.62-5.084.30.0743801.852199.6
5.08-5.814.40.06644021.772199.8
5.81-7.324.40.05944061.575199.8
7.32-504.10.05140971.259191

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3JSM

3jsm


Resolution: 2.7048→44.3 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.776 / SU ML: 0.89 / σ(F): 1.39 / Phase error: 29.65 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2676 2606 3.03 %RANDOM
Rwork0.2331 ---
obs0.2341 86138 97.09 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.761 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso max: 179.72 Å2 / Biso mean: 80.3305 Å2 / Biso min: 28.66 Å2
Baniso -1Baniso -2Baniso -3
1-3.8877 Å2-0 Å214.1031 Å2
2--7.9809 Å2-0 Å2
3---1.2917 Å2
Refinement stepCycle: LAST / Resolution: 2.7048→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15817 1810 0 0 17627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00918333
X-RAY DIFFRACTIONf_angle_d1.27425272
X-RAY DIFFRACTIONf_chiral_restr0.0932763
X-RAY DIFFRACTIONf_plane_restr0.0072874
X-RAY DIFFRACTIONf_dihedral_angle_d17.5667025
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7048-2.7540.3905960.36293270336673
2.754-2.8070.34721490.34434397454697
2.807-2.86430.34971230.32064403452698
2.8643-2.92650.37151110.31114420453198
2.9265-2.99460.33121450.30024401454698
2.9946-3.06950.32771390.28934440457998
3.0695-3.15240.33171340.27314417455199
3.1524-3.24520.30781500.2664466461699
3.2452-3.34990.29321540.25974481463599
3.3499-3.46960.31451400.26184458459899
3.4696-3.60840.29761500.24884498464899
3.6084-3.77260.26861380.24024503464199
3.7726-3.97130.27261410.226144744615100
3.9713-4.220.26811430.208345464689100
4.22-4.54550.2171510.20144864637100
4.5455-5.00240.24851510.194445284679100
5.0024-5.72490.27591220.218845474669100
5.7249-7.20770.29961300.233345624692100
7.2077-44.3060.1811390.19414235437491

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