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- PDB-2hmi: HIV-1 REVERSE TRANSCRIPTASE/FRAGMENT OF FAB 28/DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2hmi
TitleHIV-1 REVERSE TRANSCRIPTASE/FRAGMENT OF FAB 28/DNA COMPLEX
Components
  • (FAB FRAGMENT OF MONOCLONAL ANTIBODY ...) x 2
  • DNA (5'-D(*AP*TP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*C)-3')
  • DNA (5'-D(*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*A)-3')
  • HISUBUNIT OF V-1 REVERSE TRANSCRIPTASE
  • SUBUNIT OF V-1 REVERSE TRANSCRIPTASE
KeywordsIMMUNE SYSTEM/DNA / AIDS / HIV-1 / RT / POLYMERASE / IMMUNE SYSTEM-DNA COMPLEX
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 / Immunoglobulins / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsDing, J. / Arnold, E.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Structure and functional implications of the polymerase active site region in a complex of HIV-1 RT with a double-stranded DNA template-primer and an antibody Fab fragment at 2.8 A resolution.
Authors: Ding, J. / Das, K. / Hsiou, Y. / Sarafianos, S.G. / Clark Jr., A.D. / Jacobo-Molina, A. / Tantillo, C. / Hughes, S.H. / Arnold, E.
#1: Journal: Structure / Year: 1996
Title: Structure of Unliganded HIV-1 Reverse Transcriptase at 2.7 A Resolution: Implications of Conformational Changes for Polymerization and Inhibition Mechanisms
Authors: Hsiou, Y. / Ding, J. / Das, K. / Clark Junior, A.D. / Hughes, S.H. / Arnold, E.
#2: Journal: Methods Enzymol. / Year: 1995
Title: Crystallization of Human Immunodeficiency Virus Type 1 Reverse Transcriptase with and without Nucleic Acid Substrates, Inhibitors, and an Antibody Fab Fragment
Authors: Clark Junior, A.D. / Jacobo-Molina, A. / Clark, P. / Hughes, S.H. / Arnold, E.
#3: Journal: Structure / Year: 1995
Title: Structure of HIV-1 Reverse Transcriptase in a Complex with the Non-Nucleoside Inhibitor Alpha-Apa R 95845 at 2.8 A Resolution
Authors: Ding, J. / Das, K. / Tantillo, C. / Zhang, W. / Clark Junior, A.D. / Jessen, S. / Lu, X. / Hsiou, Y. / Jacobo-Molina, A. / Andries, K. / Pauwels, R. / Moereels, H. / Koymans, L. / Janssen, P. ...Authors: Ding, J. / Das, K. / Tantillo, C. / Zhang, W. / Clark Junior, A.D. / Jessen, S. / Lu, X. / Hsiou, Y. / Jacobo-Molina, A. / Andries, K. / Pauwels, R. / Moereels, H. / Koymans, L. / Janssen, P.A.J. / Smith Junior, R.H. / Koepke, M.K. / Michejda, C.J. / Hughes, S.H. / Arnold, E.
#4: Journal: Nat.Struct.Biol. / Year: 1995
Title: Structure of HIV-1 RT/TIBO R 86183 Complex Reveals Similarity in the Binding of Diverse Nonnucleoside Inhibitors
Authors: Ding, J. / Das, K. / Moereels, H. / Koymans, L. / Andries, K. / Janssen, P.A. / Hughes, S.H. / Arnold, E.
#5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Crystal Structure of Human Immunodeficiency Virus Type 1 Reverse Transcriptase Complexed with Double-Stranded DNA at 3.0 A Resolution Shows Bent DNA
Authors: Jacobo-Molina, A. / Ding, J. / Nanni, R.G. / Clark Junior, A.D. / Lu, X. / Tantillo, C. / Williams, R.L. / Kamer, G. / Ferris, A.L. / Clark, P. / Hizi, A. / Hughes, S.H. / Arnold, E.
#6: Journal: Nature / Year: 1992
Title: Structure of HIV-1 Reverse Transcriptase/DNA Complex at 7 A Resolution Showing Active Site Locations
Authors: Arnold, E. / Jacobo-Molina, A. / Nanni, R.G. / Williams, R.L. / Lu, X. / Ding, J. / Clark Junior, A.D. / Zhang, A. / Ferris, A.L. / Clark, P. / Hizi, A. / Hughes, S.H.
History
DepositionApr 10, 1998Deposition site: BNL / Processing site: NDB
SupersessionOct 14, 1998ID: 1HMI
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: DNA (5'-D(*AP*TP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*C)-3')
F: DNA (5'-D(*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*A)-3')
A: SUBUNIT OF V-1 REVERSE TRANSCRIPTASE
B: HISUBUNIT OF V-1 REVERSE TRANSCRIPTASE
C: FAB FRAGMENT OF MONOCLONAL ANTIBODY 28
D: FAB FRAGMENT OF MONOCLONAL ANTIBODY 28


Theoretical massNumber of molelcules
Total (without water)172,3476
Polymers172,3476
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.000, 169.000, 221.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Cell settingtrigonal
Space group name H-MP3212

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Components

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DNA chain , 2 types, 2 molecules EF

#1: DNA chain DNA (5'-D(*AP*TP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*C)-3')


Mass: 5864.801 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*A)-3')


Mass: 5484.528 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 2 types, 2 molecules AB

#3: Protein SUBUNIT OF V-1 REVERSE TRANSCRIPTASE / E.C.2.7.7.49 / HIV-1 RT


Mass: 64274.652 Da / Num. of mol.: 1 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: BH10 ISOLATE / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase
#4: Protein HISUBUNIT OF V-1 REVERSE TRANSCRIPTASE / E.C.2.7.7.49 / HIV-1 RT


Mass: 50281.762 Da / Num. of mol.: 1 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: BH10 ISOLATE / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase

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Antibody , 2 types, 2 molecules CD

#5: Antibody FAB FRAGMENT OF MONOCLONAL ANTIBODY 28 / FAB 28


Mass: 22984.068 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB-C
#6: Antibody FAB FRAGMENT OF MONOCLONAL ANTIBODY 28 / FAB 28


Mass: 23457.156 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C

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Details

Compound detailsHIV-1 RT IS COMPOSED OF TWO SUBUNITS OF 66 KDA AND 51 KDA, DESIGNATED AS P66 (CHAIN A) AND P51 ...HIV-1 RT IS COMPOSED OF TWO SUBUNITS OF 66 KDA AND 51 KDA, DESIGNATED AS P66 (CHAIN A) AND P51 (CHAIN B), RESPECTIVELY. IN THIS STRUCTURE, 558 AMINO ACID RESIDUES WERE TRACED FOR THE P66 SUBUNIT AND 430 AMINO ACID RESIDUES WERE LOCATED IN THE P51 SUBUNIT. THE POLYMERASE DOMAINS OF BOTH P66 AND P51 ARE COMPRISED OF FOUR SUBDOMAINS, NAMED FINGERS, PALM, THUMB, AND CONNECTION. THE BOUNDARIES OF INDIVIDUAL SUBDOMAINS ARE AS FOLLOWING: FINGERS: 1 - 84 AND 120 - 150 PALM: 85 - 119 AND 151 - 243 THUMB: 244 - 322 CONNECTION: 323 - 437 IN P66 AND 327 - 430 IN P51.
Has protein modificationY
Sequence detailsTHE BOUND DOUBLE-STRANDED DNA IS A 19-MER/18-MER TEMPLATE- PRIMER. BOTH THE TEMPLATE STRAND AND THE ...THE BOUND DOUBLE-STRANDED DNA IS A 19-MER/18-MER TEMPLATE- PRIMER. BOTH THE TEMPLATE STRAND AND THE PRIMER STRAND ARE NUMBERED IN THE 5'-3' DIRECTION. THE FIRST NUCLEOTIDE AT THE 5'-TERMINUS OF THE TEMPLATE STRAND (ADE) FORMS A ONE-BASE OVERHANG. THE DNA OLIGOMERS WERE NOT PHOSPHORYLATED AT THE 5'-TERMINUS, SO E801 AND F821 DO NOT HAVE PHOSPHORUS ATOM POSITIONS. THE FOLLOWING REGIONS ARE HIGHLY DISORDERED WITH VERY POOR ELECTRON DENSITY; THE BACKBONE TRACE IN THESE REGIONS IS TENTATIVE. P66: 64-74, 136-138, 242-253, 286-293, AND 554-558. P51: 242-252.

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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: 5.29 Å3/Da / Density % sol: 75.6 %
Description: INTENSITY-INTEGRATION SOFTWARE USED WAS A MODIFIED VERSION OF THE PURDUE OSCILLATION FILM PROCESSING PACKAGE AND DENZO
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Jacobo-Molina, A., (1991) Biochemistry, 30, 6351. / pH: 8.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mMTris1reservoirpH8.8
232.5 %satammonium sulfate1reservoir
321 mg/mlprotein1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: 1992
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionRedundancy: 4.3 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.13
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 76187 / % possible obs: 86.6 % / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
DENZOdata reduction
X-PLOR3.1refinement
RefinementResolution: 2.8→8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 100000 / Data cutoff low absF: 125 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.352 3203 5.1 %RANDOM
Rwork0.271 ---
obs-63413 74.8 %-
Displacement parametersBiso mean: 36.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a1.24 Å0.88 Å
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10894 753 0 0 11647
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg0.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.73
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
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.435 194 5.6 %
Rwork0.392 3266 -
obs--40.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2RNA-DNA.PARAMRNA-DNA.TOP
X-RAY DIFFRACTION3ADD_PROLINE.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.271
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.73

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