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- PDB-1rtd: STRUCTURE OF A CATALYTIC COMPLEX OF HIV-1 REVERSE TRANSCRIPTASE: ... -

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Entry
Database: PDB / ID: 1rtd
TitleSTRUCTURE OF A CATALYTIC COMPLEX OF HIV-1 REVERSE TRANSCRIPTASE: IMPLICATIONS FOR NUCLEOSIDE ANALOG DRUG RESISTANCE
Components
  • (PROTEIN (REVERSE ...) x 2
  • DNA PRIMER FOR REVERSE TRANSCRIPTASE
  • DNA TEMPLATE FOR REVERSE TRANSCRIPTASE
KeywordsTRANSFERASE/DNA / COMPLEX(NUCLEOTIDYLTRANSFERASE / DNA / DNTP) / PROTEIN/DNA / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / : / Budding and maturation of HIV virion / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / protein processing / 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 / peptidase 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 / identical protein binding
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
THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / Gag-Pol polyprotein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsChopra, R. / Huang, H. / Verdine, G.L. / Harrison, S.C.
CitationJournal: 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
DepositionAug 26, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 9, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: DNA TEMPLATE FOR REVERSE TRANSCRIPTASE
F: DNA PRIMER FOR REVERSE TRANSCRIPTASE
G: DNA TEMPLATE FOR REVERSE TRANSCRIPTASE
H: DNA PRIMER FOR REVERSE TRANSCRIPTASE
A: PROTEIN (REVERSE TRANSCRIPTASE)
B: PROTEIN (REVERSE TRANSCRIPTASE)
C: PROTEIN (REVERSE TRANSCRIPTASE)
D: PROTEIN (REVERSE TRANSCRIPTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,13416
Polymers260,0238
Non-polymers1,1108
Water0
1
E: DNA TEMPLATE FOR REVERSE TRANSCRIPTASE
F: DNA PRIMER FOR REVERSE TRANSCRIPTASE
A: PROTEIN (REVERSE TRANSCRIPTASE)
B: PROTEIN (REVERSE TRANSCRIPTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,5919
Polymers130,0124
Non-polymers5795
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: DNA TEMPLATE FOR REVERSE TRANSCRIPTASE
H: DNA PRIMER FOR REVERSE TRANSCRIPTASE
C: PROTEIN (REVERSE TRANSCRIPTASE)
D: PROTEIN (REVERSE TRANSCRIPTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,5427
Polymers130,0124
Non-polymers5313
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.840, 150.700, 280.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.867311, -0.203893, 0.454091), (-0.168135, -0.738639, -0.652797), (0.46851, -0.642527, 0.606348)105.42614, 197.83026, 49.99073
2given(-0.913772, -0.209856, 0.347824), (-0.089985, -0.730392, -0.677075), (0.396136, -0.649991, 0.648528)108.35632, 196.5098, 50.91177
3given(-0.893019, -0.212162, 0.396869), (-0.145042, -0.699138, -0.700121), (0.426005, -0.682783, 0.593571)107.34485, 195.3051, 54.22787
4given(-0.879189, -0.234256, 0.414911), (-0.121002, -0.732476, -0.669953), (0.460853, -0.63922, 0.615639)108.17171, 195.83237, 50.28528
5given(-0.867603, -0.244288, 0.433115), (-0.137946, -0.718579, -0.681627), (0.47774, -0.651128, 0.589743)107.86497, 196.08101, 50.30592
DetailsTHE HIV-1 REVERSE TRANSCRIPTASE CONSISTS OF TWO SUBUNITS, P66 (DESIGNATED BY CHAINS A AND C) AND P51 (DESIGNATED BY CHAINS B AND D). THE DNA DUPLEX IS COMPOSED OF TEMPLATE (DESIGNATED CHAIN E) AND PRIMER (DESIGNATED CHAIN F). THE BOUND DEOXY-THYMINE TRIPHOSPHATE HAS CHAIN IDENTIFIER A. IN THIS CRYSTAL FORM THERE ARE TWO REVERSE TRANSCRIPTASE COMPLEXES PER ASYMMETRIC UNIT. ONE MOLECULE WAS SIGNIFICANTLY BETTER ORDERED THAN THE OTHER. COORDINATES FOR BOTH MOLECULES ARE CONTAINED IN THIS ENTRY, AND THE NON-CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS GIVEN BELOW WERE THOSE USED TO GENERATE CHAINS C,D,G, AND H FROM A,B,E, AND F DURING THE COURSE OF REFINEMENT.

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Components

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DNA chain , 2 types, 4 molecules EGFH

#1: DNA chain DNA TEMPLATE FOR REVERSE TRANSCRIPTASE


Mass: 8327.361 Da / Num. of mol.: 2 / Mutation: C2-THIOL TETHER AT TEMPLATE GUANINE 11 / Source method: obtained synthetically
#2: DNA chain DNA PRIMER FOR REVERSE TRANSCRIPTASE


Mass: 6416.123 Da / Num. of mol.: 2 / Fragment: PRIMER / Mutation: C2-THIOL TETHER AT TEMPLATE GUANINE 11 / Source method: obtained synthetically

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PROTEIN (REVERSE ... , 2 types, 4 molecules ACBD

#3: Protein PROTEIN (REVERSE TRANSCRIPTASE) / E.C.2.7.7.49 / HIV-1 RT


Mass: 63869.148 Da / Num. of mol.: 2 / Fragment: P61 / Mutation: P1K, Q258C, E478Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: BH10 / Gene: POL / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase
#4: Protein PROTEIN (REVERSE TRANSCRIPTASE) / E.C.2.7.7.49 / HIV-1 RT


Mass: 51399.047 Da / Num. of mol.: 2 / Fragment: P50
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: BH10 / Gene: POL / Production host: Escherichia coli (E. coli) / References: UniProt: P04585, RNA-directed DNA polymerase

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Non-polymers , 2 types, 8 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate


Mass: 482.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N2O14P3

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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: 3.21 Å3/Da / Density % sol: 61.66 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein-DNA complex1drop
210 mMMES1drop
32 mM1dropMgCl2
4200 mM1dropNaCl
50.02 mMEDTA1drop
62.5 mMdTTP1drop
714 %(w/v)PEG60001reservoir
850 mMMES1reservoir
91 M1reservoirNaCl
1010 mM1reservoirMgCl2
110.1 mMEDTA1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: BRANDEIS - B4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.2→18 Å / Num. obs: 54281 / % possible obs: 93.8 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rsym value: 0.103 / Net I/σ(I): 11.2
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.372 / % possible all: 84.3
Reflection
*PLUS
Rmerge(I) obs: 0.103
Reflection shell
*PLUS
% possible obs: 84.3 % / Num. unique obs: 4802 / Rmerge(I) obs: 0.372

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→12 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.298 --RANDOM
Rwork0.224 ---
obs0.224 49983 92.2 %-
Refinement stepCycle: LAST / Resolution: 3.2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15852 1872 64 0 17788
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 3.2→3.3 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.385 --
Rwork0.325 3760 -
obs--81.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPH19.SOL
X-RAY DIFFRACTION2PARAM11.INTTOPH19.PEP
X-RAY DIFFRACTION3DNA-RNA_REP.PARAMTOP_NDBX.DNA
X-RAY DIFFRACTION4PARAM19.SOL

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