[English] 日本語
Yorodumi
- PDB-5txl: STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE (RT) TERNARY COMPLEX WIT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5txl
TitleSTRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE (RT) TERNARY COMPLEX WITH A DOUBLE STRANDED DNA AND AN INCOMING DATP
Components
  • (HIV-1 REVERSE TRANSCRIPTASE ...) x 2
  • DNA (5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG) P*CP*GP*CP*CP*GP)-3')
  • DNA (5'-D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP* CP*TP*GP*TP*G)-3')
KeywordsTRANSFERASE/DNA / RT / DNA / crosslink / N site complex / pyrophosphorolysis / P51 / P66 / TRANSFERASE / DRUG RESISTANCE / MUTATION / TRANSFERASE-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 / symbiont-mediated suppression of host gene expression / 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 / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / 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 / 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 / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsDas, K. / Martinez, S.M. / Arnold, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI027690 United States
Citation
Journal: Antimicrob. Agents Chemother. / Year: 2017
Title: Structural Insights into HIV Reverse Transcriptase Mutations Q151M and Q151M Complex That Confer Multinucleoside Drug Resistance.
Authors: Das, K. / Martinez, S.E. / Arnold, E.
#1: Journal: J.Biol.Chem. / Year: 2009
Title: Structural Basis For The Role Of The K65R Mutation In Hiv-1 Reverse Transcriptase Polymerization, Excision Antagonism, And Tenofovir Resistance.
Authors: Das, K. / Bandwar, R.P. / White, K.L. / Feng, J.Y. / Sarafianos, S.G. / Tuske, S. / Tu, X. / Clark, A.D. / Boyer, P.L. / Hou, X. / Gaffney, B.L. / Jones, R.A. / Miller, M.D. / Hughes, S.H. / Arnold, E.
#2: Journal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structural Basis Of Hiv-1 Resistance To Azt By Excision.
Authors: Tu, X. / Das, K. / Han, Q. / Bauman, J.D. / Clark, A.D. / Hou, X. / Frenkel, Y.V. / Gaffney, B.L. / Jones, R.A. / Boyer, P.L. / Hughes, S.H. / Sarafianos, S.G. / Arnold, E.
#3: Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: High-Resolution Structures Of Hiv-1 Reverse Transcriptase/Tmc278 Complexes: Strategic Flexibility Explains Potency Against Resistance Mutations.
Authors: Das, K. / Bauman, J.D. / Clark, A.D. / Frenkel, Y.V. / Lewi, P.J. / Shatkin, A.J. / Hughes, S.H. / Arnold, E.
#4: Journal: J.Med.Chem. / Year: 2004
Title: Roles Of Conformational And Positional Adaptability In Structure-Based Design Of Tmc125-R165335 (Etravirine) And Related Non-Nucleoside Reverse Transcriptase Inhibitors That Are Highly Potent ...Title: Roles Of Conformational And Positional Adaptability In Structure-Based Design Of Tmc125-R165335 (Etravirine) And Related Non-Nucleoside Reverse Transcriptase Inhibitors That Are Highly Potent And Effective Against Wild-Type And Drug-Resistant Hiv-1 Variants.
Authors: Das, K. / Clark, A.D. / Lewi, P.J. / Heeres, J. / De Jonge, M.R. / Koymans, L.M. / Vinkers, H.M. / Daeyaert, F. / Ludovici, D.W. / Kukla, M.J. / De Corte, B. / Kavash, R.W. / Ho, C.Y. / Ye, ...Authors: Das, K. / Clark, A.D. / Lewi, P.J. / Heeres, J. / De Jonge, M.R. / Koymans, L.M. / Vinkers, H.M. / Daeyaert, F. / Ludovici, D.W. / Kukla, M.J. / De Corte, B. / Kavash, R.W. / Ho, C.Y. / Ye, H. / Lichtenstein, M.A. / Andries, K. / Pauwels, R. / De Bethune, M.P. / Boyer, P.L. / Clark, P. / Hughes, S.H. / Janssen, P.A. / Arnold, E.
History
DepositionNov 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2Jun 7, 2017Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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_validate_close_contact / 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_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_asym.entity_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 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 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT
B: HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT
T: DNA (5'-D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP* CP*TP*GP*TP*G)-3')
P: DNA (5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG) P*CP*GP*CP*CP*GP)-3')
C: HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT
D: HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT
E: DNA (5'-D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP* CP*TP*GP*TP*G)-3')
F: DNA (5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG) P*CP*GP*CP*CP*GP)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,82022
Polymers261,6498
Non-polymers2,17114
Water3,945219
1
A: HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT
B: HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT
T: DNA (5'-D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP* CP*TP*GP*TP*G)-3')
P: DNA (5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG) P*CP*GP*CP*CP*GP)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,98912
Polymers130,8254
Non-polymers1,1648
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15720 Å2
ΔGint-83 kcal/mol
Surface area48360 Å2
MethodPISA
2
C: HIV-1 REVERSE TRANSCRIPTASE P66 SUBUNIT
D: HIV-1 REVERSE TRANSCRIPTASE P51 SUBUNIT
E: DNA (5'-D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP* CP*TP*GP*TP*G)-3')
F: DNA (5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG) P*CP*GP*CP*CP*GP)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,83110
Polymers130,8254
Non-polymers1,0066
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15300 Å2
ΔGint-64 kcal/mol
Surface area48960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.380, 133.846, 139.340
Angle α, β, γ (deg.)90.00, 97.30, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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

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


Mass: 64022.414 Da / Num. of mol.: 2 / Mutation: Q258C, C280S, D498N
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 / Mutation: C280S
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, DNA-directed DNA polymerase

-
DNA chain , 2 types, 4 molecules TEPF

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


Mass: 8383.385 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SYNTHESIZED / Source: (synth.) Human immunodeficiency virus 1
#4: DNA chain DNA (5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG) P*CP*GP*CP*CP*GP)-3')


Mass: 6490.267 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SYNTHESIZED / Source: (synth.) Human immunodeficiency virus 1

-
Sugars , 1 types, 2 molecules

#5: 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

-
Non-polymers , 5 types, 231 molecules

#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#9: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: PEG 8000, AMMONIUM SULFATE, MGCL2, GLYCEROL, SUCROSE
PH range: 6.8 -7.2

-
Data collection

DiffractionMean temperature: 104 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 111859 / % possible obs: 98.7 % / Observed criterion σ(I): -1 / Redundancy: 4.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.6
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.53 / CC1/2: 0.619 / % possible all: 88.1

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V4I

3v4i


Resolution: 2.501→48.075 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2245 3349 3 %Random
Rwork0.1927 ---
obs0.1937 111811 98.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.501→48.075 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15824 1802 135 219 17980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00618432
X-RAY DIFFRACTIONf_angle_d0.89925389
X-RAY DIFFRACTIONf_dihedral_angle_d15.84810742
X-RAY DIFFRACTIONf_chiral_restr0.0532767
X-RAY DIFFRACTIONf_plane_restr0.0062876
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5011-2.53690.29851220.3013897X-RAY DIFFRACTION85
2.5369-2.57470.32961430.29434282X-RAY DIFFRACTION93
2.5747-2.6150.33521230.28824359X-RAY DIFFRACTION97
2.615-2.65780.29141410.27084535X-RAY DIFFRACTION99
2.6578-2.70370.29291400.27984483X-RAY DIFFRACTION99
2.7037-2.75280.28061320.26964584X-RAY DIFFRACTION100
2.7528-2.80580.26911520.25554545X-RAY DIFFRACTION100
2.8058-2.8630.27831290.24194584X-RAY DIFFRACTION100
2.863-2.92530.27991560.23234563X-RAY DIFFRACTION100
2.9253-2.99330.26271380.22084552X-RAY DIFFRACTION100
2.9933-3.06820.23571450.22234580X-RAY DIFFRACTION100
3.0682-3.15110.27131370.23084561X-RAY DIFFRACTION100
3.1511-3.24380.24081470.2184587X-RAY DIFFRACTION100
3.2438-3.34850.26071480.21414561X-RAY DIFFRACTION100
3.3485-3.46810.23481340.20944583X-RAY DIFFRACTION100
3.4681-3.60690.2371440.19784574X-RAY DIFFRACTION100
3.6069-3.7710.23951460.1924583X-RAY DIFFRACTION100
3.771-3.96980.19311370.17894565X-RAY DIFFRACTION100
3.9698-4.21830.23211360.16654590X-RAY DIFFRACTION100
4.2183-4.54380.17241400.16034583X-RAY DIFFRACTION100
4.5438-5.00060.19311390.15484629X-RAY DIFFRACTION100
5.0006-5.72320.19571220.1714606X-RAY DIFFRACTION100
5.7232-7.20680.23441580.19484582X-RAY DIFFRACTION99
7.2068-48.08370.17211400.15334494X-RAY DIFFRACTION95
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0010.02990.01340.00650.01010.0140.1965-0.0110.0719-0.22260.03740.00320.0138-0.1408-01.1397-0.2811-0.02730.75910.15220.4735-13.42416.124818.7589
2-0.0031-0.01440.04630.05730.01210.00450.28640.25940.1724-0.22910.02830.0866-0.0187-0.0550.05121.8609-0.3377-0.21811.08230.45120.9688-14.432227.842121.5344
30.0744-0.03170.03220.0344-0.0573-0.00220.17870.09120.4743-0.236-0.0477-0.15970.12550.04930.01731.0303-0.3938-0.02240.55470.0980.3295-8.473320.773929.2812
40.0524-0.0302-0.0660.1658-0.05530.13440.21490.13920.5098-0.63960.2008-0.2935-0.24980.07510.32821.1306-0.47780.18660.64540.0440.62133.836321.723937.2898
50.12510.1113-0.00940.1936-0.13630.1951-0.0435-0.2350.0753-0.25880.2170.0196-0.5362-0.12990.04010.6468-0.21260.04690.127-0.04530.7626-20.598626.944756.8983
60.00630.0242-0.03360.02040.01280.05040.0977-0.07890.2472-0.0610.00610.2246-0.28220.0178-00.3891-0.06150.00130.254-0.08790.5113-18.029114.46365.9584
70.0744-0.0808-0.05550.2420.09870.0650.0406-0.0224-0.0666-0.0018-0.04790.111-0.0890.1222-0.01760.2845-0.0743-0.05230.3185-0.13420.3541-16.29344.077569.0204
80.19260.0359-0.19530.1543-0.05210.1287-0.0958-0.05690.1583-0.09240.0870.0859-0.0495-0.069500.19240.0215-0.06020.3918-0.02780.4203-45.5828-4.677673.6538
90.0901-0.0518-0.05170.03320.02080.09440.07510.08320.0987-0.1131-0.04690.15770.0097-0.2778-00.26460.0116-0.05580.3864-0.07660.4816-46.0952-8.008774.3105
100.03610.0288-0.03380.00230.02140.00420.1630.21490.0864-0.2054-0.0993-0.04490.12460.17750.00820.4984-0.3278-0.150.3368-0.30550.2764-10.1971-7.912934.5033
110.720.053-0.13710.29730.11440.3278-0.19370.1735-0.2764-0.31710.3174-0.1994-0.05660.39240.01290.5288-0.1410.10110.4753-0.15920.4521-2.8104-14.860941.6956
120.00360.051-0.05290.23260.1161-0.0075-0.0292-0.1098-0.18210.15290.1213-0.02270.13410.22780.01040.31030.09930.00860.5704-0.08060.6086-14.1898-27.850662.5256
130.0885-0.1749-0.17470.31810.09220.1313-0.268-0.0172-0.08840.08740.0320.10590.34890.0455-0.15320.352-0.06780.04090.2257-0.13280.4357-31.0031-26.768366.1455
140.13680.0050.07240.18750.06040.1195-0.1598-0.0261-0.0448-0.06760.04860.1573-0.0173-0.0334-0.14720.2719-0.0806-0.02830.3309-0.11350.3992-17.7363-13.868457.4678
150.00260.00640.00520.00550.00620.00230.114-0.005-0.01830.01490.056-0.0434-0.0164-0.039601.3066-0.0633-0.34270.93180.27060.9063-24.356827.197230.2617
160.0059-0.00840.0033-0.01590.01290.01550.041-0.01290.0278-0.34380.03550.314-0.17730.0619-00.815-0.2354-0.15630.7860.16580.814-26.028313.113546.4217
170.0046-0.00040.00070.0040.00580.00580.03990.0198-0.0443-0.05940.02930.05940.07880.064601.2593-0.29280.09240.992-0.00211.1262-37.7454-7.178249.922
180.00820.00780.00010.00170.00060.0069-0.0344-0.04-0.0516-0.0426-0.0758-0.0048-0.0106-0.0506-01.0561-0.5149-0.21041.16190.02231.3022-52.143-14.62854.9896
190.0134-0.03010.00630.025-0.00390.00790.15020.00670.1614-0.2855-0.1207-0.2477-0.0825-0.108300.6553-0.2053-0.14170.7877-0.01880.7741-43.6573-7.460251.2715
200.00690.0026-0.02430.00580.00770.0121-0.19220.02150.0862-0.17070.00690.0882-0.21860.0338-01.0704-0.22980.00270.78330.27131.0326-23.337517.142843.7301
210.35290.09580.02990.3545-0.31630.59320.53710.59220.9757-0.2967-0.1220.5445-0.2517-0.250.3651.25030.26890.05610.6929-0.0141-0.6113-26.8168-46.4852-2.5295
220.7069-0.06960.05780.59650.13740.5515-0.014-0.1843-0.0626-0.17420.08270.0267-0.1105-0.13210.04280.2304-0.0355-0.05690.2609-0.05590.2663-31.5336-56.883242.5509
230.1197-0.08230.07580.1604-0.04620.02840.25140.1050.033-0.4641-0.2326-0.09180.2640.36340.03410.8490.1360.21970.5368-0.01320.4384-3.7324-59.55938.3538
240.0327-0.0103-0.02030.00140.01960.01950.0351-0.0643-0.0324-0.20020.0383-0.14120.1530.380200.71230.22920.12670.78060.01130.58410.1656-66.165319.4728
250.07040.0765-0.04810.1783-0.0780.047-0.26950.13640.0506-0.8773-0.06620.01780.14190.8343-0.27840.42120.64190.64811.11080.10380.18277.2623-66.101217.3863
260.0448-0.00450.14070.0885-0.11070.07830.23160.05520.0477-0.0016-0.0997-0.12020.19890.17050.02570.16010.15480.08140.52910.02090.35072.2109-67.945242.3228
270.1618-0.1710.2810.2431-0.24340.23240.1213-0.0659-0.1683-0.188-0.2034-0.03860.10510.0108-0.00010.31560.07170.00150.3653-0.01290.3766-12.1999-74.915650.3078
280.0496-0.00270.00510.13380.03120.0557-0.0063-0.03820.1159-0.2365-0.24780.11980.13980.404-0.00370.3990.07460.03640.5049-0.05430.3631-9.1599-63.588233.3541
290.0029-0.0017-00.0020.00350.00190.0627-0.00730.0020.12-0.02460.01240.04410.0221-00.9872-0.08-0.10350.9275-0.18160.5988-39.4004-55.4948-6.1853
300.00180.0064-0.0126-0.00820.02240.00710.4722-0.0286-0.0717-0.14860.01080.14520.2037-0.077401.0985-0.1352-0.06750.83130.07210.6436-32.2575-57.54813.9888
310.0012-0.0125-0.00670.02160.0310.01270.2002-0.0205-0.24680.0199-0.0969-0.16140.1612-0.047301.009-0.1077-0.09320.88650.14841.4403-30.3632-79.799333.875
320.00110.00080.00490.00210.00150.0013-0.05940.00110.0433-0.0309-0.07620.01330.0032-0.019-01.4233-0.10140.18041.0857-0.25851.3438-31.3531-87.492132.8668
33-0.00950.02210.0207-0.0196-0.02390.01240.19520.2115-0.1553-0.4297-0.20230.236-0.0860.051300.8739-0.0675-0.08010.485-0.02080.3718-33.0513-64.418520.3005
340.00570.0018-0.0006-0.0029-0.00210.0004-0.01030.03580.0427-0.0787-0.02890.1039-0.02240.0041-01.20630.2244-0.06981.12010.12480.5304-31.2681-45.74463.96
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 83 )
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 143 )
4X-RAY DIFFRACTION4chain 'A' and (resid 144 through 226 )
5X-RAY DIFFRACTION5chain 'A' and (resid 227 through 325 )
6X-RAY DIFFRACTION6chain 'A' and (resid 326 through 363 )
7X-RAY DIFFRACTION7chain 'A' and (resid 364 through 421 )
8X-RAY DIFFRACTION8chain 'A' and (resid 422 through 515 )
9X-RAY DIFFRACTION9chain 'A' and (resid 516 through 554 )
10X-RAY DIFFRACTION10chain 'B' and (resid 4 through 27 )
11X-RAY DIFFRACTION11chain 'B' and (resid 28 through 194 )
12X-RAY DIFFRACTION12chain 'B' and (resid 195 through 269 )
13X-RAY DIFFRACTION13chain 'B' and (resid 270 through 363 )
14X-RAY DIFFRACTION14chain 'B' and (resid 364 through 428 )
15X-RAY DIFFRACTION15chain 'T' and (resid 702 through 706 )
16X-RAY DIFFRACTION16chain 'T' and (resid 707 through 716 )
17X-RAY DIFFRACTION17chain 'T' and (resid 717 through 721 )
18X-RAY DIFFRACTION18chain 'T' and (resid 722 through 725 )
19X-RAY DIFFRACTION19chain 'P' and (resid 803 through 812 )
20X-RAY DIFFRACTION20chain 'P' and (resid 813 through 822 )
21X-RAY DIFFRACTION21chain 'C' and (resid -1 through 325 )
22X-RAY DIFFRACTION22chain 'C' and (resid 326 through 554 )
23X-RAY DIFFRACTION23chain 'D' and (resid 4 through 59 )
24X-RAY DIFFRACTION24chain 'D' and (resid 60 through 99 )
25X-RAY DIFFRACTION25chain 'D' and (resid 100 through 194 )
26X-RAY DIFFRACTION26chain 'D' and (resid 195 through 269 )
27X-RAY DIFFRACTION27chain 'D' and (resid 270 through 363 )
28X-RAY DIFFRACTION28chain 'D' and (resid 364 through 428 )
29X-RAY DIFFRACTION29chain 'E' and (resid 702 through 706 )
30X-RAY DIFFRACTION30chain 'E' and (resid 707 through 716 )
31X-RAY DIFFRACTION31chain 'E' and (resid 717 through 725 )
32X-RAY DIFFRACTION32chain 'F' and (resid 803 through 807 )
33X-RAY DIFFRACTION33chain 'F' and (resid 808 through 818 )
34X-RAY DIFFRACTION34chain 'F' and (resid 819 through 822 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more