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- PDB-5hro: STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE In COMPLEX WITH A DNA ap... -

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Basic information

Entry
Database: PDB / ID: 5hro
TitleSTRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE In COMPLEX WITH A DNA aptamer and an Alpha-carboxy nucleoside phosphonate inhibitor (alpha-CNP)
Components
  • (HIV-1 REVERSE TRANSCRIPTASE ...) x 2
  • DNA (38-MER)
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / RT / DNA APTAMER / NCRTI / nucleotide-competing RT inhibitor / 2-O-METHYLCYTIDINE / P51 / P66 / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


RNA-directed DNA polymerase activity / 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 ...RNA-directed DNA polymerase activity / 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 / telomerase activity / viral penetration into host nucleus / RNA stem-loop binding / 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 / symbiont entry into host cell / viral translational frameshifting / lipid binding / 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
sucrose / Chem-3JY / DNA / DNA (> 10) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsDas, K. / Arnold, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI27690 United States
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Conformational States of HIV-1 Reverse Transcriptase for Nucleotide Incorporation vs Pyrophosphorolysis-Binding of Foscarnet.
Authors: Das, K. / Balzarini, J. / Miller, M.T. / Maguire, A.R. / DeStefano, J.J. / Arnold, E.
History
DepositionJan 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Aug 31, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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 / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_asym.entity_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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 / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id

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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
E: DNA (38-MER)
C: HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT
D: HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT
F: DNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,23622
Polymers255,1056
Non-polymers2,13116
Water905
1
A: HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT
B: HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT
E: DNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,81013
Polymers127,5523
Non-polymers1,25810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13310 Å2
ΔGint-136 kcal/mol
Surface area46370 Å2
MethodPISA
2
C: HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT
D: HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT
F: DNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,4269
Polymers127,5523
Non-polymers8746
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12440 Å2
ΔGint-73 kcal/mol
Surface area46630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.245, 128.959, 131.049
Angle α, β, γ (deg.)90.00, 101.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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HIV-1 REVERSE TRANSCRIPTASE ... , 2 types, 4 molecules ACBD

#1: Protein HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT / Pr160Gag-Pol


Mass: 63875.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
Strain: isolate BH10 / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase
#2: Protein HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT / Pr160Gag-Pol


Mass: 51928.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
Strain: isolate BH10 / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase

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DNA chain / Sugars , 2 types, 4 molecules EF

#3: DNA chain DNA (38-MER)


Mass: 11748.526 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 19 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-3JY / [(1R)-2-methoxy-1-{[(1S,3R)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclopentyl]oxy}-2-oxoethyl]phosphonic acid


Mass: 362.272 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N2O8P
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.96 Å3/Da / Density % sol: 58.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 7% PEG 8000, 100 MM BISTRIS-PROPANE, AMMONIUM SULFATE, 5% GLYCEROL, 5% SUCROSE
PH range: 6.8 - 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 2.75→40 Å / Num. obs: 74312 / % possible obs: 95.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 73.52 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.043 / Rrim(I) all: 0.088 / Χ2: 1.583 / Net I/av σ(I): 18.737 / Net I/σ(I): 12.5 / Num. measured all: 268023
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.75-2.82.50.532187.9
2.8-2.852.70.507190.3
2.85-2.92.80.484192.4
2.9-2.962.90.438193.1
2.96-3.0330.386193.1
3.03-3.13.10.336194.4
3.1-3.173.20.29194.4
3.17-3.263.30.247195.2
3.26-3.363.40.196195.6
3.36-3.463.50.162196.3
3.46-3.593.70.133196.5
3.59-3.733.80.116197.2
3.73-3.93.90.096198.4
3.9-4.1140.082198.5
4.11-4.364.10.073199.1
4.36-4.74.30.068199.6
4.7-5.174.40.066199.4
5.17-5.924.50.069199.5
5.92-7.454.50.058199.5
7.45-404.30.046191.8

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data collection
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D3G

5d3g


Resolution: 2.75→38.52 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.17
RfactorNum. reflection% reflectionSelection details
Rfree0.2646 2915 3.98 %Random selection
Rwork0.2348 ---
obs0.2361 73226 95.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.75→38.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15776 1440 128 5 17349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01117957
X-RAY DIFFRACTIONf_angle_d0.74524668
X-RAY DIFFRACTIONf_dihedral_angle_d15.38210484
X-RAY DIFFRACTIONf_chiral_restr0.0472692
X-RAY DIFFRACTIONf_plane_restr0.0052844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.79510.34611070.35943130X-RAY DIFFRACTION89
2.7951-2.84330.36731300.34873163X-RAY DIFFRACTION91
2.8433-2.8950.40111240.33233209X-RAY DIFFRACTION93
2.895-2.95060.34211390.31433249X-RAY DIFFRACTION93
2.9506-3.01090.34171220.30533269X-RAY DIFFRACTION93
3.0109-3.07630.35951340.29763282X-RAY DIFFRACTION94
3.0763-3.14780.27951330.29533286X-RAY DIFFRACTION94
3.1478-3.22650.32891370.29073319X-RAY DIFFRACTION95
3.2265-3.31370.32091290.27773331X-RAY DIFFRACTION96
3.3137-3.41110.29891340.26443362X-RAY DIFFRACTION96
3.4111-3.52120.30831580.25413334X-RAY DIFFRACTION97
3.5212-3.64690.25361390.25223385X-RAY DIFFRACTION97
3.6469-3.79280.2841490.24263429X-RAY DIFFRACTION98
3.7928-3.96530.28481420.24233420X-RAY DIFFRACTION99
3.9653-4.17410.23451450.23033440X-RAY DIFFRACTION99
4.1741-4.43530.22981670.22033456X-RAY DIFFRACTION99
4.4353-4.77710.25781410.20613502X-RAY DIFFRACTION99
4.7771-5.25680.23111540.20813487X-RAY DIFFRACTION100
5.2568-6.0150.2761410.22873506X-RAY DIFFRACTION99
6.015-7.56880.271520.2233487X-RAY DIFFRACTION100
7.5688-38.52420.20451380.17723265X-RAY DIFFRACTION91

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