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- PDB-6kdj: HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:lamivudine... -

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Basic information

Entry
Database: PDB / ID: 6kdj
TitleHIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:lamivudine 5'-triphosphate ternary complex
Components
  • DNA/RNA (38-MER)
  • HIV-1 RT p51 subunit
  • HIV-1 reverse transcriptase p66 subunit
KeywordsTRANSFERASE/DNA / Lamivudine 5'-TRIPHOSPHATE / HIV-1 / HBV / reverse transcriptase / drug resistance / drug sensitivity / TRANSFERASE-DNA complex / REPLICATION
Function / homology
Function and homology information


phosphatidylinositol-4,5-bisphosphate binding / induction by virus of host apoptotic process => GO:0019051 / 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 ...phosphatidylinositol-4,5-bisphosphate binding / induction by virus of host apoptotic process => GO:0019051 / 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 / establishment of integrated proviral latency / viral penetration into host nucleus / 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 / lipid binding / DNA-directed DNA polymerase activity / aspartic-type endopeptidase activity / suppression by virus of host gene expression / viral entry into host cell / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / RNA binding / DNA binding / zinc ion binding / membrane / metal ion binding / 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 domain / Reverse transcriptase connection / Reverse transcriptase thumb domain / Reverse transcriptase thumb / 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 domain / Reverse transcriptase connection / Reverse transcriptase thumb domain / Reverse transcriptase thumb / 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. / gag gene protein p17 (matrix protein) / Immunodeficiency lentiviral matrix, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / Retropepsin-like catalytic domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Reverse transcriptase domain / RNase H type-1 domain profile. / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, N-terminal / Zinc knuckle / zinc finger / Zinc finger, CCHC-type superfamily / Zinc finger CCHC-type profile. / Zinc finger, CCHC-type / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Pol protein / sucrose / DNA (> 10) / DNA / Lamivudine Triphosphate / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Human immunodeficiency virus type 1
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsYasutake, Y. / Hattori, S.I. / Tamura, N. / Maeda, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP19fk0310113 Japan
CitationJournal: Sci Rep / Year: 2020
Title: Structural features in common of HBV and HIV-1 resistance against chirally-distinct nucleoside analogues entecavir and lamivudine.
Authors: Yasutake, Y. / Hattori, S.I. / Tamura, N. / Matsuda, K. / Kohgo, S. / Maeda, K. / Mitsuya, H.
History
DepositionJul 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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_conn_angle / 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.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_asym.entity_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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 RT p51 subunit
E: DNA/RNA (38-MER)
C: HIV-1 reverse transcriptase p66 subunit
D: HIV-1 RT p51 subunit
F: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,01715
Polymers255,3196
Non-polymers1,6989
Water4,486249
1
A: HIV-1 reverse transcriptase p66 subunit
B: HIV-1 RT p51 subunit
E: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,6798
Polymers127,6593
Non-polymers1,0205
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12480 Å2
ΔGint-38 kcal/mol
Surface area46840 Å2
MethodPISA
2
C: HIV-1 reverse transcriptase p66 subunit
D: HIV-1 RT p51 subunit
F: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,3377
Polymers127,6593
Non-polymers6784
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11800 Å2
ΔGint-45 kcal/mol
Surface area47260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)285.114, 285.114, 96.004
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein HIV-1 reverse transcriptase p66 subunit


Mass: 64033.387 Da / Num. of mol.: 2 / Mutation: Y214F, F215Y, Q250M, C261S, C379S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pCDF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: D3XFN5, UniProt: P12497*PLUS
#2: Protein HIV-1 RT p51 subunit / HIV-1 reverse transcriptase p51 subunit / p51 RT


Mass: 51861.547 Da / Num. of mol.: 2 / Mutation: C749S, C867S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P12497

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DNA chain / Sugars , 2 types, 3 molecules EF

#3: DNA chain DNA/RNA (38-MER)


Mass: 11764.525 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.: 1
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, 257 molecules

#5: Chemical ChemComp-1RZ / Lamivudine Triphosphate / Lamivudine-5'-triphosphate / 3TC Triphosphate / [[(2R,5S)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 469.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H14N3O12P3S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Mg
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.94 Å3/Da / Density % sol: 58.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: BIS-TRIS-HCL, DI-AMMONIUM HYDROGEN CITRATE, MGCL2, PEG 6000, SUCROSE, GLYCEROL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.51→50 Å / Num. obs: 99368 / % possible obs: 99.9 % / Redundancy: 5.3 % / Rrim(I) all: 0.105 / Net I/σ(I): 10.6
Reflection shellResolution: 2.51→2.55 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4930 / Rrim(I) all: 0.853 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XN1
Resolution: 2.51→48.787 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 23.91
RfactorNum. reflection% reflection
Rfree0.23 5031 5.06 %
Rwork0.1817 --
obs0.1841 99346 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.51→48.787 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15690 1501 103 249 17543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00917902
X-RAY DIFFRACTIONf_angle_d1.04624626
X-RAY DIFFRACTIONf_dihedral_angle_d24.9786855
X-RAY DIFFRACTIONf_chiral_restr0.0612672
X-RAY DIFFRACTIONf_plane_restr0.0072834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5101-2.53860.31641780.25023128X-RAY DIFFRACTION100
2.5386-2.56850.33681600.25213153X-RAY DIFFRACTION100
2.5685-2.59980.32421830.2463139X-RAY DIFFRACTION100
2.5998-2.63270.27241390.23983161X-RAY DIFFRACTION100
2.6327-2.66730.26421880.23643169X-RAY DIFFRACTION100
2.6673-2.70390.31021510.23273139X-RAY DIFFRACTION100
2.7039-2.74250.28121480.22793170X-RAY DIFFRACTION100
2.7425-2.78340.26871510.22163124X-RAY DIFFRACTION100
2.7834-2.82690.2851900.21653137X-RAY DIFFRACTION100
2.8269-2.87330.3011780.21743130X-RAY DIFFRACTION100
2.8733-2.92280.27781780.21123142X-RAY DIFFRACTION100
2.9228-2.97590.28791750.21053151X-RAY DIFFRACTION100
2.9759-3.03320.25821920.21063112X-RAY DIFFRACTION100
3.0332-3.09510.29791670.2093176X-RAY DIFFRACTION100
3.0951-3.16240.25191620.20153158X-RAY DIFFRACTION100
3.1624-3.23590.28641780.19773119X-RAY DIFFRACTION100
3.2359-3.31680.25011600.19113155X-RAY DIFFRACTION100
3.3168-3.40650.27361610.18483136X-RAY DIFFRACTION100
3.4065-3.50670.2131650.18323130X-RAY DIFFRACTION100
3.5067-3.61980.26141810.17713145X-RAY DIFFRACTION100
3.6198-3.74920.2231560.1763136X-RAY DIFFRACTION100
3.7492-3.89920.22131730.17783171X-RAY DIFFRACTION99
3.8992-4.07660.20621810.16753088X-RAY DIFFRACTION99
4.0766-4.29140.20291740.15823137X-RAY DIFFRACTION100
4.2914-4.56010.18841590.15563152X-RAY DIFFRACTION100
4.5601-4.91190.20831620.15973161X-RAY DIFFRACTION100
4.9119-5.40560.18231640.15793132X-RAY DIFFRACTION100
5.4056-6.18650.22921560.18913154X-RAY DIFFRACTION100
6.1865-7.78920.19491770.17753130X-RAY DIFFRACTION100
7.7892-48.79610.17931440.15293180X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.24470.0355-0.40130.80390.12963.1718-0.0669-0.13140.07230.03410.0403-0.10920.2360.15650.01880.25390.00710.04220.3765-0.02530.3414178.7293276.4553-146.6513
23.33650.51940.52321.35030.93583.138-0.1360.18440.3264-0.2483-0.10610.4911-0.2755-0.89320.22430.36730.0614-0.05570.6334-0.01480.4919146.4027277.169-155.6121
31.74580.31080.52934.77342.86546.4039-0.1104-0.3855-0.334-0.1339-0.02320.21790.441-0.61980.15020.3449-0.03330.0550.44030.01410.3482175.2398265.2737-148.2154
42.25030.0954-0.33052.0184-0.69461.3338-0.07840.21940.16-0.23830.07250.1118-0.0376-0.10780.00590.2917-0.03290.00070.4053-0.02960.2673211.7988282.7436-183.7068
51.0213-0.56870.19863.1071-1.01311.30660.01790.03790.0329-0.0248-0.064-0.21760.02180.37580.04270.2917-0.04750.02690.47530.00040.3044239.345263.3938-182.569
63.78820.66710.35483.1129-0.88023.67110.20520.6784-0.4289-0.5718-0.4625-0.32840.56760.27080.23970.47380.01280.07840.5374-0.04190.362208.0256274.7377-191.69
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 553)
2X-RAY DIFFRACTION2(chain 'B' and resid 5 through 427)
3X-RAY DIFFRACTION3(chain 'E' and resid -1 through 33)
4X-RAY DIFFRACTION4(chain 'C' and resid 1 through 553)
5X-RAY DIFFRACTION5(chain 'D' and resid 5 through 427)
6X-RAY DIFFRACTION6(chain 'F' and resid -4 through 33)

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