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- PDB-3v81: Crystal structure of HIV-1 reverse transcriptase (RT) with DNA an... -

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Basic information

Entry
Database: PDB / ID: 3v81
TitleCrystal structure of HIV-1 reverse transcriptase (RT) with DNA and the nonnucleoside inhibitor nevirapine
Components
  • DNA (5'-D(*A*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 / P51/P66 / hetero dimer / NNRTI / nonnucleoside inhibitor / AIDS / DNA / recombination / RNA-directed DNA polymerase / viramune / DNA polymerase / endonuclease / hydrolase / multifunctional enzyme / transferase / TRANSFERASE-DNA complex / AZT / ZIDOVUDINE
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA 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. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H 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
Chem-NVP / DNA / DNA (> 10) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 BH10
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8503 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.
#6: Journal: Nat.Struct.Biol. / Year: 1995
Title: High resolution structures of HIV-1 RT from four RT-inhibitor complexes.
Authors: Ren, J. / Esnouf, R. / Garman, E. / Somers, D. / Ross, C. / Kirby, I. / Keeling, J. / Darby, G. / Jones, Y. / Stuart, D.
History
DepositionDec 22, 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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(*A*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(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(ATM))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,47010
Polymers257,9378
Non-polymers5332
Water00
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(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(ATM))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,2355
Polymers128,9694
Non-polymers2661
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12410 Å2
ΔGint-50 kcal/mol
Surface area50900 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(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(ATM))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,2355
Polymers128,9694
Non-polymers2661
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12300 Å2
ΔGint-47 kcal/mol
Surface area51300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.822, 132.052, 142.732
Angle α, β, γ (deg.)90.00, 100.84, 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: Q258C, C280S, D498N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 BH10
Strain: BH10 ISOLATE / 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
Strain: BH10 isolate / 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(*A*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
#5: Chemical ChemComp-NVP / 11-CYCLOPROPYL-5,11-DIHYDRO-4-METHYL-6H-DIPYRIDO[3,2-B:2',3'-E][1,4]DIAZEPIN-6-ONE / NON-NUCLEOSIDE RT INHIBITOR NEVIRAPINE


Mass: 266.298 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H14N4O / Comment: medication*YM
Has protein modificationY

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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: 3.22 Å3/Da / Density % sol: 61.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.8
Details: PEG 8000, ammonium sulfate, sucrose, glycerol, magnesium chloride, Bis-Tris propane , 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: Mar 13, 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: 2.85→40 Å / Num. obs: 75389 / % possible obs: 99 % / Observed criterion σ(I): -1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.09 / Χ2: 1.214 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.85-2.92.90.61837061.088197.7
2.9-2.9530.57736531.131198.1
2.95-3.013.10.52237751.129198.5
3.01-3.073.10.50637581.165198.8
3.07-3.143.20.40837411.196199
3.14-3.213.30.37437681.26199.1
3.21-3.293.40.32137651.28199.5
3.29-3.383.50.26937671.311199.5
3.38-3.483.60.21338221.295199.6
3.48-3.593.70.17337871.339199.7
3.59-3.723.80.13737951.308199.7
3.72-3.873.90.11237651.293199.7
3.87-4.043.90.09238031.284199.6
4.04-4.2640.07537861.251199.7
4.26-4.524.10.06438041.202199.6
4.52-4.874.10.05937891.2199.6
4.87-5.364.10.05738211.073199.8
5.36-6.134.10.0638421.151199.8
6.13-7.724.20.05738391.201199.8
7.72-4040.05536031.087192.1

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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 3V6D

3v6d


Resolution: 2.8503→38.413 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7429 / SU ML: 0.94 / σ(F): 0 / Phase error: 32.52 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.298 2287 3.03 %
Rwork0.2505 --
obs0.252 75359 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.013 Å2 / ksol: 0.293 e/Å3
Displacement parametersBiso max: 199.74 Å2 / Biso mean: 82.9103 Å2 / Biso min: 18.31 Å2
Baniso -1Baniso -2Baniso -3
1--2.1261 Å20 Å22.7078 Å2
2--5.1163 Å2-0 Å2
3----2.9902 Å2
Refinement stepCycle: LAST / Resolution: 2.8503→38.413 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15824 1646 40 0 17510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118152
X-RAY DIFFRACTIONf_angle_d1.33724992
X-RAY DIFFRACTIONf_chiral_restr0.0912718
X-RAY DIFFRACTIONf_plane_restr0.0072878
X-RAY DIFFRACTIONf_dihedral_angle_d18.5566950
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8503-2.91230.44951210.39124322444393
2.9123-2.980.4281350.36354517465298
2.98-3.05450.35821510.35024544469599
3.0545-3.1370.35431370.33254582471999
3.137-3.22930.34051490.30664529467899
3.2293-3.33350.34531630.29044595475899
3.3335-3.45250.3421420.273546144756100
3.4525-3.59070.32841510.259545904741100
3.5907-3.7540.26571380.245646194757100
3.754-3.95170.27091410.227845744715100
3.9517-4.1990.25651510.21146054756100
4.199-4.52280.24971570.202646164773100
4.5228-4.9770.26531450.203546344779100
4.977-5.69520.26981340.214646394773100
5.6952-7.16770.32821290.250746594788100
7.1677-38.41660.26581430.22494433457693

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