[English] 日本語
Yorodumi
- PDB-3suf: Crystal structure of NS3/4A protease variant D168A in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3suf
TitleCrystal structure of NS3/4A protease variant D168A in complex with MK-5172
ComponentsNS3 protease, NS4A protein
KeywordsHYDROLASE/INHIBITOR / drug resistance / drug design / Protease inhibitors / HCV / serine protease / VIRAL PROTEIN / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / lipid droplet / protein complex oligomerization ...host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / lipid droplet / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / induction by virus of host autophagy / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / RNA binding / zinc ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Thrombin, subunit H - #120 / : / Hepatitis C virus core protein, chain A superfamily / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b ...Thrombin, subunit H - #120 / : / Hepatitis C virus core protein, chain A superfamily / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural protein NS2 / Hepatitis C virus, Non-structural 5a protein / Hepatitis C virus, Non-structural 5a protein, domain 1a / Hepatitis C virus non-structural 5a, 1B domain / NS5A domain 1a superfamily / Hepatitis C virus non-structural 5a protein membrane anchor / Hepatitis C virus non-structural 5a zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Trypsin-like serine proteases / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Thrombin, subunit H / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Chem-SUE / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsSchiffer, C.A. / Romano, K.P.
CitationJournal: Plos Pathog. / Year: 2012
Title: The Molecular Basis of Drug Resistance against Hepatitis C Virus NS3/4A Protease Inhibitors.
Authors: Romano, K.P. / Ali, A. / Aydin, C. / Soumana, D. / Ozen, A. / Deveau, L.M. / Silver, C. / Cao, H. / Newton, A. / Petropoulos, C.J. / Huang, W. / Schiffer, C.A.
History
DepositionJul 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Dec 11, 2019Group: Advisory / Database references / Structure summary
Category: chem_comp / pdbx_distant_solvent_atoms / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _struct_ref_seq_dif.details
Revision 1.4Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NS3 protease, NS4A protein
B: NS3 protease, NS4A protein
C: NS3 protease, NS4A protein
D: NS3 protease, NS4A protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,32713
Polymers85,9024
Non-polymers3,4259
Water2,540141
1
A: NS3 protease, NS4A protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3083
Polymers21,4751
Non-polymers8322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NS3 protease, NS4A protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4044
Polymers21,4751
Non-polymers9283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NS3 protease, NS4A protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3083
Polymers21,4751
Non-polymers8322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: NS3 protease, NS4A protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3083
Polymers21,4751
Non-polymers8322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.004, 103.560, 73.510
Angle α, β, γ (deg.)90.00, 112.04, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
NS3 protease, NS4A protein


Mass: 21475.385 Da / Num. of mol.: 4
Fragment: NS4A (UNP residues 1674-1688), NS3 (UNP residues 1027-1208)
Mutation: A1027S, P1028G, I1029D, L1039E, L1040E, I1043Q, I1044E, L1047Q, A1066T, C1073S, C1078L, I1098T, P1112Q, S1165A, C1185S, C1679S, V1686I, D1168A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus / Strain: subtype 1a, BID-V318 / Gene: NS3-NS4A / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8DG50
#2: Chemical
ChemComp-SUE / (1aR,5S,8S,10R,22aR)-5-tert-butyl-N-{(1R,2S)-1-[(cyclopropylsulfonyl)carbamoyl]-2-ethenylcyclopropyl}-14-methoxy-3,6-di oxo-1,1a,3,4,5,6,9,10,18,19,20,21,22,22a-tetradecahydro-8H-7,10-methanocyclopropa[18,19][1,10,3,6]dioxadiazacyclononadec ino[11,12-b]quinoxaline-8-carboxamide / Grazoprevir, MK-5172


Mass: 766.903 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H50N6O9S / Comment: protease inhibitor*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsMK-5172 IS A MACROCYCLIC, PEPTIDOMIMETIC HCV NS3/4A PROTEASE INHIBITOR FROM MERCK. THE DRUG MIMICS ...MK-5172 IS A MACROCYCLIC, PEPTIDOMIMETIC HCV NS3/4A PROTEASE INHIBITOR FROM MERCK. THE DRUG MIMICS THE PEPTIDE BACKBONE OF PROTEINS, ALTHOUGH THE DRUG MOIETIES CANNOT BE SEQUENCED USING AMINO ACID NOMENCLATURE.
Sequence detailsTHE COFACTOR 4A RESIDUES 990-1000 (GLY SER VAL VAL ILE VAL GLY ARG ILE ASN LEU) IN THIS ENTRY ...THE COFACTOR 4A RESIDUES 990-1000 (GLY SER VAL VAL ILE VAL GLY ARG ILE ASN LEU) IN THIS ENTRY CORRESPOND TO RESIDUES NUMBERING 1678-1688 OF DATABASE SEQUENCE REFERENCE (UNP A8DG50). THIS PEPTIDE IS COVALENTLY LINKED TO THE N-TERMINUS OF NS3. C1679S MUTATION WAS ENGINEERED TO PREVENT DISULFIDE FORMATION. THE V1686I AND I1687N WERE ENGINEERED TO OPTIMIZE THE LINKER BETWEEN THE COFACTOR 4A AND NS3.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 295 K / Method: hanging drop, vapor diffusion / pH: 6.2
Details: 20-25% PEG 3350, 0.1M MES (pH 6.5), 4% ammonium sulfate, hanging drop, vapor diffusion, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97872 Å
DetectorDate: Apr 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.568
11-H, -K, H+L20.432
ReflectionResolution: 2.19→30 Å / Num. obs: 37671 / % possible obs: 95.9 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.19-2.282.70.389194.5
2.28-2.372.70.339195
2.37-2.482.70.29194.8
2.48-2.612.80.246195.4
2.61-2.772.80.193196.3
2.77-2.992.90.134197
2.99-3.2930.104196.7
3.29-3.7630.074196.5
3.76-4.7330.053196.5
4.73-3030.038196.6

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→29.22 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.9 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.076 / SU ML: 0.197 / SU R Cruickshank DPI: 0.0624 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25932 1865 5 %RANDOM
Rwork0.19877 ---
obs0.20184 35743 94.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.325 Å2
Baniso -1Baniso -2Baniso -3
1-14 Å20 Å2-7.34 Å2
2---2.85 Å20 Å2
3----11.15 Å2
Refinement stepCycle: LAST / Resolution: 2.19→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5303 0 225 141 5669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.025640
X-RAY DIFFRACTIONr_bond_other_d0.0080.023572
X-RAY DIFFRACTIONr_angle_refined_deg1.3942.0077755
X-RAY DIFFRACTIONr_angle_other_deg1.3473.0098767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8795746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.66222.97165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.40615756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6821532
X-RAY DIFFRACTIONr_chiral_restr0.0740.2946
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216290
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021082
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3941.53735
X-RAY DIFFRACTIONr_mcbond_other0.0881.51557
X-RAY DIFFRACTIONr_mcangle_it0.68925990
X-RAY DIFFRACTIONr_scbond_it1.09331905
X-RAY DIFFRACTIONr_scangle_it1.6784.51729
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.19→2.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 109 -
Rwork0.209 2070 -
obs--73.99 %
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)
12.64630.20490.50312.41170.09040.2814-0.17590.07860.0957-0.36970.0712-0.12170.168-0.13580.10470.2271-0.0449-0.15530.0182-0.0090.26519.6709-6.52970.46
215.45099.2631-2.90024.1826-5.1631.45310.1886-0.98570.2173-0.0169-0.18070.16830.18060.4435-0.0080.315-0.0568-0.17570.1216-0.00910.26053.6624-6.8918-1.345
32.5253-0.8922-2.0687-6.47971.75671.1681-0.1707-0.88180.3840.4866-0.09630.1576-0.2178-0.63330.2670.4029-0.0076-0.12970.31330.00850.3326-2.6148-13.649411.271
4-1.9804-3.0845.01483.00393.1063-2.84530.4642-0.1582-0.63990.0316-0.40990.0649-0.2114-0.1108-0.05430.2556-0.1047-0.22680.1512-0.00660.3398.6347-14.3841.8307
510.4613-4.663-7.0447-0.5259-3.126313.648-0.0157-0.28780.1860.11970.261-0.0261-0.03980.3309-0.24520.2061-0.0181-0.09550.0642-0.03060.22937.5158-5.89887.295
62.7282-0.2744-0.04141.80420.03360.96160.0632-0.0039-0.2320.1102-0.00240.14310.0894-0.0649-0.06080.2161-0.005-0.10120.1130.02540.198211.9987-5.557710.1182
71.0581-1.3125-2.04562.56721.71021.3024-0.06120.03290.03930.0862-0.04280.07650.1132-0.06550.1040.12840.0297-0.07570.12890.00580.168314.0718-4.404315.5263
817.8473-9.9278-4.09179.587812.12672.8967-0.13-0.3637-0.25520.52740.17240.1863-0.1031-0.9283-0.04240.3822-0.0527-0.12510.17940.01250.15417.4316-9.035318.3001
92.55241.60561.20412.06172.18592.0742-0.03010.0894-0.2074-0.2060.198-0.1694-0.0777-0.0751-0.16790.2557-0.0187-0.17030.12770.0390.203912.9256-13.255117.6783
100.6817-1.36051.0248-1.416-1.97861.83490.28870.004-0.0392-0.1959-0.1083-0.12560.0143-0.299-0.18040.2466-0.0198-0.08650.05970.04860.191116.0602-7.503416.7114
11-0.3654-0.8403-0.50330.9290.42570.3971-0.00320.11910.0137-0.09010.04790.0037-0.04790.082-0.04470.1658-0.0476-0.15070.1383-0.00140.26422.7019-3.37693.1168
124.15531.20242.61651.2369-0.14462.8244-0.1423-0.26030.0264-0.01220.148-0.0071-0.0558-0.0988-0.00570.1969-0.0147-0.1060.1106-0.01960.2817.80037.08363.2769
137.8899-2.82211.27680.47351.69413.43070.211-0.1575-0.26160.02630.20140.3902-0.51-0.2992-0.41240.199-0.0595-0.06380.1102-0.01850.267719.660613.50745.9845
142.6241-0.0208-2.32844.8294-0.39064.68670.09770.2157-0.0555-0.09890.00840.2773-0.2314-0.3525-0.10610.1499-0.0017-0.160.1-0.00230.22910.34217.35747.1776
158.73791.9385-5.92111.9497-0.93824.8843-0.1344-0.3238-0.0965-0.22790.1647-0.1964-0.13740.0582-0.03030.15980.0119-0.13280.1026-0.01470.231523.42870.32544.0146
160.46150.09371.432910.9508-1.22-1.7705-0.0661-0.26810.34160.6715-0.0365-0.1279-0.25830.24180.10260.26380.0498-0.14270.2059-0.0220.260414.64814.494512.3069
171.4234-0.82172.4384-0.6549-2.25483.2356-0.0436-0.35320.1262-0.1040.1292-0.23820.2574-0.0189-0.08560.23790.0326-0.13110.137-0.04010.313523.39993.307912.2195
180.8379-1.2246-4.097823.3308-9.56961.88940.24510.1808-0.962-0.3596-0.362-1.1158-0.11741.0440.11690.25420.0702-0.26680.35060.07810.395526.3772-7.180616.7483
190.05140.1732-2.79233.50882.2225-1.2516-0.394-0.03360.09840.25230.313-0.2288-0.02950.14020.0810.1750.0431-0.12050.1294-0.05170.2632-21.656625.615212.1779
200.3802-1.2678-0.05681.727-0.97245.0181-0.1424-0.2783-0.18260.40470.25730.0532-0.09450.1181-0.11490.2005-0.0279-0.14620.1990.09350.3168-21.574523.881319.4479
21-0.3119-1.2088-2.53532.2873-0.8156-0.7077-0.3359-0.08280.1040.37310.40280.0313-0.34970.0813-0.06690.25870.0809-0.18380.110.00260.308-21.58932.07813.0357
223.3546-0.44-1.8768-0.79780.28533.7633-0.1489-0.3737-0.1533-0.0961-0.11790.23010.2028-0.45290.26680.2192-0.0116-0.16180.04840.04360.3668-22.723720.79739.4656
23-3.217-2.8950.5884-1.4519-0.09753.0074-0.08450.1486-0.00950.01920.0767-0.01590.03450.18250.00780.2005-0.0057-0.11290.06480.01760.2414-10.801224.00378.8081
241.4327-0.89741.25951.5942-2.3774-0.6950.16470.1065-0.1214-0.2067-0.08040.12770.1641-0.1229-0.08430.1689-0.0305-0.11390.1070.01240.2874-18.753622.13380.7365
252.4624-0.9301-0.94870.92622.77332.12570.11130.06550.3805-0.1629-0.1595-0.2763-0.3978-0.24890.04820.22910.0316-0.09840.07990.01930.2477-18.338834.32173.2359
265.93113.8943-1.38065.681-4.31743.16830.2101-0.0399-0.0532-0.3348-0.4146-0.1640.24840.02960.20450.1756-0.0168-0.11280.0907-0.00160.2154-9.871320.1341-3.2828
27-0.26640.4188-0.2308-4.1894-1.1511-0.7845-0.15140.02540.13-0.19750.2349-0.3288-0.3207-0.0894-0.08350.2579-0.0528-0.1560.1327-0.03760.3304-12.933929.29175.7183
281.6655-1.59692.0218-0.0957-2.71190.7861-0.1949-0.12240.03710.23230.0649-0.10210.05480.08070.130.24790.079-0.15030.137-0.00580.3338-1.027620.069615.3428
297.163-3.2226-3.89393.95161.43150.4169-0.4455-0.0619-0.68330.3759-0.02440.1312-0.2807-0.34930.46990.30280.0803-0.16230.22010.08180.3056-12.733612.130518.2907
3011.8604-3.4194-14.83683.5984.179213.6859-0.0840.2984-0.08610.0228-0.01770.3513-0.0815-0.18040.10170.17860.0118-0.17260.18920.03570.2186-4.95946.556615.0657
310.91453.02543.60125.8869-0.89720.9331-0.1531-0.2312-0.0636-0.2180.084-0.24860.6214-0.07650.06910.29070.0612-0.1260.14780.01170.2502-9.97743.351411.8688
324.53114.35011.77037.09881.05321.16250.2486-0.0942-0.5660.20450.02020.01840.0549-0.0961-0.26880.16520.0119-0.09810.09250.03370.331-14.576512.099812.8483
332.38541.34974.32193.1431-1.70315.5079-0.2537-0.10490.0588-0.14750.05230.0474-0.31050.0910.20130.15730.0136-0.0690.1721-0.01630.2132-5.902714.580412.0595
3428.549815.0043-5.05785.3637-1.6656-8.4217-0.4241-0.0493-0.2447-0.6631-0.0025-0.3044-0.0148-0.20830.42660.2812-0.0262-0.09060.1383-0.01330.2875-14.375-1.14568.0447
357.89382.04126.44663.19951.8287-2.77070.251-0.110.13120.9336-0.17080.4555-0.14410.1122-0.08020.3284-0.069-0.04490.1001-0.00760.1941-5.486812.89256.3453
368.1178-3.9359-2.92697.98112.74727.0632-0.0746-0.41860.1529-0.2001-0.101-0.9124-0.2372-0.09210.17560.1656-0.0427-0.11150.0619-0.00040.2836-1.126922.20372.0051
373.37571.34620.34790.16891.7893-2.78410.13830.05040.1866-0.08570.08660.07790.25480.2796-0.22490.19550.0552-0.10790.0667-0.01140.23851.773-6.8127-16.1821
38-2.874311.2062-5.11275.9011-1.45675.37140.1506-0.6307-0.3340.1045-0.1046-0.1207-0.3232-0.2522-0.0460.2593-0.0142-0.22420.37420.10780.3101-6.2861-10.194-2.5679
3914.85422.4889-6.40995.43854.81879.86290.30250.8317-0.21360.0893-0.2469-0.1388-0.5131-0.3486-0.05570.15940.0576-0.17410.11240.04890.22615.9458-6.3479-10.0434
406.80811.71720.05271.1572-1.7246-0.631-0.0076-0.1236-0.0865-0.1039-0.1131-0.3064-0.0090.1940.12070.3070.046-0.09360.11840.01480.29958.2963-8.6835-18.3012
41-0.7864-2.3262-4.513418.2993-1.44726.874-0.36170.1158-0.1047-0.01440.2780.04730.0581-0.46920.08370.10250.0129-0.15860.11880.06190.2256-3.7283-8.6816-13.5863
420.72684.4706-0.176612.52713.8767-6.56650.1584-0.50780.0511-0.1396-0.1435-0.3272-0.19060.5777-0.01490.2097-0.0801-0.10630.2890.01610.30320.44931.9429-19.4721
431.45020.6960.17090.06540.49740.0609-0.0174-0.0223-0.04050.14840.0404-0.26270.081-0.129-0.02310.22950.016-0.10660.0819-0.01290.217-7.9482-7.1285-22.2998
44-0.10211.05922.06361.11071.29990.4487-0.12550.0805-0.0221-0.0880.1908-0.0909-0.0210.2008-0.06530.23540.0574-0.13420.1863-0.00390.23810.7795-10.7566-27.5303
455.2706-2.28981.75724.6343-1.77162.40740.15360.161-0.1949-0.1742-0.1090.16180.11330.0481-0.04460.22160.0213-0.1170.0946-0.01770.1809-8.9654-7.1488-27.1652
461.6058-0.03830.81360.56310.74221.22230.0211-0.4175-0.02020.2532-0.0757-0.00580.118-0.04560.05460.2585-0.0748-0.1260.16630.0210.2267-14.1535-9.5188-10.5758
47-1.027-0.5625-4.8432.7513-0.2254-1.1738-0.0394-0.4139-0.1192-0.1742-0.20460.0105-0.7205-0.44630.24410.25430.0199-0.16550.115-0.01420.2288-21.9139-2.2294-8.3639
484.00891.53866.11671.89212.1522.50260.20110.2393-0.19310.09420.00030.2620.251-0.0715-0.20140.2225-0.0695-0.12850.19720.03150.2308-23.41341.2632-11.6714
490.4925-4.0055-0.50133.98112.2315-1.9486-0.2606-0.4567-0.08250.22620.1966-0.13850.17240.0120.0640.2636-0.0462-0.12910.16170.01210.2124-11.65957.4644-8.4943
50-1.48610.20890.33842.77640.2073-2.7998-0.11640.25630.00570.03870.24070.11760.1813-0.1331-0.12430.3068-0.0801-0.15090.20310.01850.2589-15.1504-7.759-10.9827
512.01390.4864-1.872411.4722-3.44921.5572-0.1857-0.02090.0802-0.5190.318-0.07760.1442-0.264-0.13230.20840.0039-0.18290.09640.00580.2276-16.8916-2.2191-15.9257
521.6728-0.25260.8819-7.3791-3.9568-1.27440.0482-0.02930.1211-0.06780.06470.2508-0.2532-0.0354-0.11290.2237-0.0342-0.06870.1216-0.02820.271-19.00773.207-15.05
53-4.6669-0.0155.6187-1.49712.80662.26830.06020.2551-0.2302-0.3541-0.0869-0.11840.47390.18110.02670.48720.0016-0.0650.1846-0.10710.3838-18.3595-13.332-26.9153
54-0.88292.7852-3.8230.22850.4312-1.6149-0.3596-0.1050.18130.18640.0722-0.1002-0.3224-0.19990.28750.2951-0.0106-0.19620.2204-0.03510.29640.688822.5724-34.4999
55-0.2042.5286-2.86440.83592.38540.495-0.13690.17360.3123-0.05080.0452-0.045-0.07780.02970.09170.3293-0.0936-0.14080.18590.06360.3415-0.828924.2182-43.927
56-0.6513-0.2666-3.46131.44640.2768-1.90070.14260.10240.0565-0.1509-0.2474-0.23640.30740.45220.10480.2859-0.0084-0.22370.30220.00510.38448.983122.3474-29.6975
572.14-2.69950.63219.4537-5.19657.79670.0030.2836-0.12260.3006-0.24830.02660.01061.09660.24530.2471-0.1008-0.12950.1127-0.05140.36110.216317.0628-31.6619
58-4.50126.89461.86713.26634.35187.85630.37350.23760.0851-0.6667-0.59160.243-0.1280.4110.21820.3179-0.0058-0.11060.13460.00330.259-6.715223.1394-31.3682
591.1237-1.1860.82220.7336-0.00031.8720.2180.13870.34780.2612-0.3231-0.0655-0.08850.17220.10510.2412-0.049-0.13960.0811-0.0090.2593-7.279520.7059-25.4694
601.8368-4.3901-0.60641.78460.3666-1.29120.13480.12980.27720.099-0.13780.1418-0.05490.530.0030.3282-0.1091-0.20470.374-0.0070.23712.719124.5416-21.5991
61-2.74280.33482.94560.11562.8918.02640.0047-0.1689-0.0907-0.02550.24650.101-0.1189-0.121-0.25120.2616-0.017-0.12670.10030.03010.2503-11.767719.9706-19.8916
627.25621.1434.34460.4390.32542.73620.08690.32270.19370.0278-0.0901-0.09480.41970.59010.00320.3768-0.0507-0.16850.15380.01530.3723-4.797529.7831-28.3298
632.5899-0.87282.63824.7229-1.4122-0.74220.06430.17350.16490.27490.00650.29540.0494-0.2491-0.07080.31860.0328-0.0660.12860.030.2671-21.443826.7633-37.9614
64-1.15842.54370.05531.9611-2.3142.6134-0.06350.2505-0.1337-0.0068-0.0686-0.1741-0.06440.01760.13210.27650.0037-0.09750.0851-0.03230.2193-15.791917.7043-41.4081
65-1.30161.45015.975811.98634.79821.56170.0861-0.3428-0.68130.5864-0.42780.41270.1139-0.08750.34170.2088-0.0575-0.12510.17090.0510.3381-23.471614.9408-36.7248
662.20844.19662.04742.59973.10796.96830.03480.26030.1531-0.0862-0.0587-0.0316-0.12820.10790.02390.24930.0442-0.11530.12490.00560.2088-11.200710.202-39.0446
6713.01261.1677-4.36342.0816-6.2538.922-0.02630.2016-0.0740.1822-0.0760.18930.50820.0550.10230.3288-0.0099-0.09970.0219-0.0650.2384-16.949326.4619-39.2623
681.19333.71420.28522.30030.03582.76650.0168-0.1542-0.02070.37780.0338-0.1361-0.0865-0.2778-0.05050.15420.0207-0.08560.1064-0.0030.2444-16.566118.0182-32.8957
69-0.5481-1.83441.412112.96412.23363.47820.00920.09230.0727-0.1768-0.540.9204-0.077-0.53440.53080.15780.0021-0.07650.072-0.05670.2523-19.207110.9253-34.5638
70-4.3622.3548-2.8085-9.18940.829721.2924-0.0354-0.27020.15050.15-0.44940.36980.2114-0.41470.48470.3580.0532-0.14130.1593-0.0590.3372-17.224327.4565-23.2765
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A990 - 1005
2X-RAY DIFFRACTION2A1006 - 1012
3X-RAY DIFFRACTION3A1013 - 1024
4X-RAY DIFFRACTION4A1025 - 1032
5X-RAY DIFFRACTION5A1033 - 1038
6X-RAY DIFFRACTION6A1039 - 1051
7X-RAY DIFFRACTION7A1052 - 1057
8X-RAY DIFFRACTION8A1058 - 1064
9X-RAY DIFFRACTION9A1065 - 1079
10X-RAY DIFFRACTION10A1080 - 1086
11X-RAY DIFFRACTION11A1087 - 1108
12X-RAY DIFFRACTION12A1109 - 1121
13X-RAY DIFFRACTION13A1122 - 1130
14X-RAY DIFFRACTION14A1131 - 1142
15X-RAY DIFFRACTION15A1143 - 1154
16X-RAY DIFFRACTION16A1155 - 1165
17X-RAY DIFFRACTION17A1166 - 1173
18X-RAY DIFFRACTION18A1174 - 1179
19X-RAY DIFFRACTION19B990 - 998
20X-RAY DIFFRACTION20B999 - 1019
21X-RAY DIFFRACTION21B1020 - 1032
22X-RAY DIFFRACTION22B1033 - 1042
23X-RAY DIFFRACTION23B1043 - 1053
24X-RAY DIFFRACTION24B1054 - 1064
25X-RAY DIFFRACTION25B1065 - 1074
26X-RAY DIFFRACTION26B1075 - 1081
27X-RAY DIFFRACTION27B1082 - 1089
28X-RAY DIFFRACTION28B1090 - 1103
29X-RAY DIFFRACTION29B1104 - 1112
30X-RAY DIFFRACTION30B1113 - 1119
31X-RAY DIFFRACTION31B1120 - 1133
32X-RAY DIFFRACTION32B1134 - 1144
33X-RAY DIFFRACTION33B1145 - 1157
34X-RAY DIFFRACTION34B1158 - 1166
35X-RAY DIFFRACTION35B1167 - 1172
36X-RAY DIFFRACTION36B1173 - 1179
37X-RAY DIFFRACTION37C990 - 998
38X-RAY DIFFRACTION38C999 - 1007
39X-RAY DIFFRACTION39C1008 - 1012
40X-RAY DIFFRACTION40C1013 - 1031
41X-RAY DIFFRACTION41C1032 - 1036
42X-RAY DIFFRACTION42C1037 - 1043
43X-RAY DIFFRACTION43C1044 - 1061
44X-RAY DIFFRACTION44C1062 - 1075
45X-RAY DIFFRACTION45C1076 - 1088
46X-RAY DIFFRACTION46C1089 - 1112
47X-RAY DIFFRACTION47C1113 - 1119
48X-RAY DIFFRACTION48C1120 - 1128
49X-RAY DIFFRACTION49C1129 - 1137
50X-RAY DIFFRACTION50C1138 - 1148
51X-RAY DIFFRACTION51C1149 - 1159
52X-RAY DIFFRACTION52C1160 - 1172
53X-RAY DIFFRACTION53C1173 - 1179
54X-RAY DIFFRACTION54D990 - 1000
55X-RAY DIFFRACTION55D1001 - 1012
56X-RAY DIFFRACTION56D1014 - 1032
57X-RAY DIFFRACTION57D1033 - 1041
58X-RAY DIFFRACTION58D1042 - 1049
59X-RAY DIFFRACTION59D1050 - 1059
60X-RAY DIFFRACTION60D1060 - 1074
61X-RAY DIFFRACTION61D1075 - 1083
62X-RAY DIFFRACTION62D1084 - 1094
63X-RAY DIFFRACTION63D1095 - 1106
64X-RAY DIFFRACTION64D1107 - 1119
65X-RAY DIFFRACTION65D1120 - 1128
66X-RAY DIFFRACTION66D1129 - 1141
67X-RAY DIFFRACTION67D1142 - 1148
68X-RAY DIFFRACTION68D1149 - 1159
69X-RAY DIFFRACTION69D1160 - 1171
70X-RAY DIFFRACTION70D1172 - 1179

+
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://pdbjlvh1.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