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- PDB-4dg1: Crystal structure of HIV-1 reverse transcriptase (RT) with polymo... -

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Basic information

Entry
Database: PDB / ID: 4dg1
TitleCrystal structure of HIV-1 reverse transcriptase (RT) with polymorphism mutation K172A and K173A
Components(Reverse Transcriptase ...) x 2
KeywordsTRANSFERASE / Polymorphism 172K / P51/P66 / HETERO DIMER / AIDS / HIV / RESISTANCE MUTATIONS / right-hand configuration / RNase H domain / Reverse transcriptase / ribonuclease H / RNA-DIRECTED DNA POLYMERASE / DNA POLYMERASE / AZT excision / AZT unblocking / nevirapine / efavirenz / AZT / NUCLEOSIDE INHIBITORS / Nonnucleoside Inhibitors / NRTI / NNRTI
Function / homology
Function and homology information


HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / 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 / 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 / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA 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. / 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
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsTu, X. / Kirby, K.A. / Marchand, B. / Sarafianos, S.G.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: HIV-1 Reverse Transcriptase (RT) Polymorphism 172K Suppresses the Effect of Clinically Relevant Drug Resistance Mutations to Both Nucleoside and Non-nucleoside RT Inhibitors.
Authors: Hachiya, A. / Marchand, B. / Kirby, K.A. / Michailidis, E. / Tu, X. / Palczewski, K. / Ong, Y.T. / Li, Z. / Griffin, D.T. / Schuckmann, M.M. / Tanuma, J. / Oka, S. / Singh, K. / Kodama, E.N. / Sarafianos, S.G.
History
DepositionJan 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Sep 12, 2012Group: Database references
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.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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Reverse Transcriptase P66 subunit
B: Reverse Transcriptase P51 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,63226
Polymers113,1142
Non-polymers1,51924
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10350 Å2
ΔGint-11 kcal/mol
Surface area45810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.230, 72.150, 109.240
Angle α, β, γ (deg.)90.00, 97.52, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-815-

HOH

21A-829-

HOH

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Components

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Reverse Transcriptase ... , 2 types, 2 molecules AB

#1: Protein Reverse Transcriptase P66 subunit


Mass: 63202.234 Da / Num. of mol.: 1 / Mutation: K172A, K173A, C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: BH10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase
#2: Protein Reverse Transcriptase P51 subunit


Mass: 49911.359 Da / Num. of mol.: 1 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: BH10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase

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Non-polymers , 4 types, 302 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O

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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: 2.75 Å3/Da / Density % sol: 55.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 50 mM bis-tris, 100 mM ammonium sulfate, 10% glycerol, 12% PEG 8000, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Apr 6, 2010
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→29.077 Å / Num. all: 65991 / Num. obs: 65991 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 42 Å2 / Rsym value: 0.051 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.15-2.272.90.4241.42851597000.42499.7
2.27-2.430.3082.42742891460.30899.6
2.4-2.5730.1953.92609286270.19599.4
2.57-2.783.10.1335.32441179740.13399.2
2.78-3.043.10.0838.52243173200.08399
3.04-3.43.10.05810.92047866290.05898.7
3.4-3.933.10.04612.91805458260.04698.2
3.93-4.813.10.03517.21527549150.03597.5
4.81-6.83.10.04141182737900.0497.1
6.8-29.0773.10.03217.4640520640.03294.7

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
PHASERphasing
CNS1.3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KLI

3kli


Resolution: 2.15→29.077 Å / Occupancy max: 1 / Occupancy min: 0.67 / FOM work R set: 0.8216 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.74 / Phase error: 25.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 3339 5.06 %RANDOM
Rwork0.2318 ---
obs0.2326 65924 98.39 %-
all-67003 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.406 Å2 / ksol: 0.325 e/Å3
Displacement parametersBiso max: 141.5 Å2 / Biso mean: 49.9241 Å2 / Biso min: 16.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.7172 Å2-0 Å2-3.0602 Å2
2---2.7126 Å20 Å2
3---0.9954 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.3 Å
Luzzati d res low-30 Å
Luzzati sigma a0.28 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.15→29.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7872 0 96 278 8246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098165
X-RAY DIFFRACTIONf_angle_d1.31311065
X-RAY DIFFRACTIONf_chiral_restr0.0981194
X-RAY DIFFRACTIONf_plane_restr0.011387
X-RAY DIFFRACTIONf_dihedral_angle_d15.8083075
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.18070.2931550.300826272782100
2.1807-2.21320.30551500.300125942744100
2.2132-2.24780.34781430.32392615275899
2.2478-2.28470.31441350.30972599273499
2.2847-2.3240.32581450.28382636278199
2.324-2.36630.27971100.27262641275199
2.3663-2.41180.32271420.26632626276899
2.4118-2.4610.27711330.27432592272599
2.461-2.51450.27711570.25912598275599
2.5145-2.57290.29641450.24512654279999
2.5729-2.63720.26931290.2492600272999
2.6372-2.70850.27251470.26032573272099
2.7085-2.78810.28551130.26392689280299
2.7881-2.8780.24321460.26442588273499
2.878-2.98080.26011480.25752608275699
2.9808-3.10.27741400.25382584272498
3.1-3.24090.2321470.24232601274898
3.2409-3.41150.22361430.2152590273398
3.4115-3.62490.2221260.21052648277498
3.6249-3.90420.22581350.20952551268697
3.9042-4.2960.21851490.18952562271197
4.296-4.9150.21451300.19542604273497
4.915-6.18260.2431250.2372610273596
6.1826-29.07930.23061460.20952595274195

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