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- PDB-1hmv: THE STRUCTURE OF UNLIGANDED REVERSE TRANSCRIPTASE FROM THE HUMAN ... -

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Entry
Database: PDB / ID: 1hmv
TitleTHE STRUCTURE OF UNLIGANDED REVERSE TRANSCRIPTASE FROM THE HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
Components
  • HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P51)
  • HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P66)
KeywordsNUCLEOTIDYLTRANSFERASE
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / 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 / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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 / 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
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 3.2 Å
AuthorsRodgers, D.W. / Gamblin, S.J. / Harris, B.A. / Ray, S. / Culp, J.S. / Hellmig, B. / Woolf, D.J. / Debouck, C. / Harrison, S.C.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: The structure of unliganded reverse transcriptase from the human immunodeficiency virus type 1.
Authors: Rodgers, D.W. / Gamblin, S.J. / Harris, B.A. / Ray, S. / Culp, J.S. / Hellmig, B. / Woolf, D.J. / Debouck, C. / Harrison, S.C.
#1: Journal: Arch.Biochem.Biophys. / Year: 1989
Title: Recombinant HIV-1 Reverse Transcriptase: Purification, Primary Structure, and Polymerase(Slash)Ribonuclease H Activities
Authors: Misrahi, V. / Lazarus, G.M. / Miles, L.M. / Meyers, C.A. / Debouck, C.
History
DepositionDec 15, 1994Processing site: BNL
Revision 1.0Mar 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P66)
B: HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P51)
C: HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P66)
D: HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P51)
E: HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P66)
F: HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P51)
G: HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P66)
H: HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P51)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)463,64912
Polymers463,5528
Non-polymers974
Water00
1
A: HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P66)
B: HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P51)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,9123
Polymers115,8882
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-32 kcal/mol
Surface area44370 Å2
MethodPISA
2
C: HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P66)
D: HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P51)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,9123
Polymers115,8882
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-32 kcal/mol
Surface area44350 Å2
MethodPISA
3
E: HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P66)
F: HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P51)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,9123
Polymers115,8882
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-32 kcal/mol
Surface area44390 Å2
MethodPISA
4
G: HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P66)
H: HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P51)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,9123
Polymers115,8882
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-32 kcal/mol
Surface area44370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.700, 162.800, 331.800
Angle α, β, γ (deg.)90.00, 105.70, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.999509, -0.012508, -0.028729), (0.013127, 0.999683, 0.021478), (0.028425, -0.021845, 0.999356)-36.57, 39.73, 163.69
2given(-0.999975, -0.000599, 0.006987), (0.000476, -0.999845, -0.017611), (0.006997, -0.017607, 0.99982)78.06, 246.89, 1.39
3given(-0.99828, -0.014789, 0.056728), (0.011128, -0.997868, -0.064314), (0.057558, -0.063572, 0.996316)25.03, 299.67999, 166.91
DetailsTHE HIV-1 REVERSE TRANSCRIPTASE CONSISTS OF TWO SUBUNITS, P66 (DESIGNATED CHAIN A) AND P51 (DESIGNATED CHAIN B). IN THIS CRYSTAL FORM THERE ARE FOUR REVERSE TRANSCRIPTASE MOLECULES PER ASYMMETRIC UNIT. COORDINATES FOR ONE MOLECULE ARE CONTAINED IN THIS ENTRY, AND THE NON-CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS GIVEN BELOW ARE BASED ON THE BEST SUPERPOSITION OF THIS MOLECULE ON EACH OF THE REMAINING THREE. MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD COORDINATES FOR THE OTHER THREE MOLECULES PRESENT IN THE ASYMMETRIC UNIT. APPLIED TO WILL GENERATE MTRIX RESIDUES RESIDUES M1 A 1 .. A 554 C 1 .. C 554 M1 B 5 .. B 427 D 5 .. D 427 M2 A 1 .. A 554 E 1 .. E 554 M2 B 5 .. B 427 F 5 .. F 427 M3 A 1 .. A 554 G 1 .. G 554 M3 B 5 .. B 427 H 5 .. H 427

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Components

#1: Protein
HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P66)


Mass: 64517.027 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: HIV-1 POL / Plasmid: POTSKF33 GENE: HIV-1 POL / Gene (production host): HIV-1 POL / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase
#2: Protein
HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P51)


Mass: 51371.035 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: HIV-1 POL / Plasmid: POTSKF33 GENE: HIV-1 POL / Gene (production host): HIV-1 POL / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
Compound detailsTHE SECONDARY STRUCTURAL ELEMENTS WERE DEFINED BASED ON HYDROGEN BONDING PATTERNS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.73 Å3/Da / Density % sol: 73.99 %
Crystal
*PLUS
Density % sol: 74 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlenzyme1drop
275 mMsodium phosphate1drop
31-2 mMdithiothreitol1drop
433-35 %ammonium sulfate1reservoir
5100 mMsodium phospahte1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 120337 / % possible obs: 85 %
Reflection
*PLUS
Highest resolution: 3.2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.133

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3.2→6 Å / σ(F): 2
RfactorNum. reflection
Rfree0.297 -
Rwork0.254 -
obs0.254 100641
Refinement stepCycle: LAST / Resolution: 3.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29592 0 4 0 29596
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg
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
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.245
X-RAY DIFFRACTIONx_dihedral_angle_deg20.7

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