[English] 日本語
Yorodumi
- PDB-3rc5: Molecular mechanisms of viral and host-cell substrate recognition... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rc5
TitleMolecular mechanisms of viral and host-cell substrate recognition by HCV NS3/4A protease
Components
  • NS3/4A protease
  • Product MAVS
KeywordsHydrolase/Hydrolase Inhibitor / drug resistance / drug design / Protease inhibitors / serine protease / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


positive regulation of IP-10 production / regulation of peroxisome organization / positive regulation of hexokinase activity / symbiont-mediated perturbation of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of myeloid dendritic cell cytokine production / CARD domain binding / viral capsid assembly ...positive regulation of IP-10 production / regulation of peroxisome organization / positive regulation of hexokinase activity / symbiont-mediated perturbation of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of myeloid dendritic cell cytokine production / CARD domain binding / viral capsid assembly / positive regulation of response to cytokine stimulus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / protein localization to mitochondrion / positive regulation of type I interferon-mediated signaling pathway / adhesion receptor-mediated virion attachment to host cell / hepacivirin / TBC/RABGAPs / peroxisomal membrane / TRAF6 mediated IRF7 activation / host cell mitochondrial membrane / host cell lipid droplet / negative regulation of viral genome replication / cytoplasmic pattern recognition receptor signaling pathway / type I interferon-mediated signaling pathway / symbiont-mediated transformation of host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction / cellular response to exogenous dsRNA / positive regulation of cytokinesis / positive regulation of NLRP3 inflammasome complex assembly / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / TRAF6 mediated NF-kB activation / positive regulation of interferon-alpha production / host cell membrane / positive regulation of type I interferon production / negative regulation of protein secretion / ubiquitin ligase complex / positive regulation of defense response to virus by host / signaling adaptor activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / antiviral innate immune response / serine-type peptidase activity / endoplasmic reticulum-Golgi intermediate compartment membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / activation of innate immune response / positive regulation of interferon-beta production / protein serine/threonine kinase binding / positive regulation of interleukin-8 production / Negative regulators of DDX58/IFIH1 signaling / molecular condensate scaffold activity / DDX58/IFIH1-mediated induction of interferon-alpha/beta / mitochondrial membrane / PKR-mediated signaling / Evasion by RSV of host interferon responses / SH3 domain binding / positive regulation of interleukin-6 production / positive regulation of protein import into nucleus / kinase binding / positive regulation of tumor necrosis factor production / SARS-CoV-1 activates/modulates innate immune responses / Ovarian tumor domain proteases / host cell / nucleoside-triphosphate phosphatase / channel activity / viral nucleocapsid / TRAF3-dependent IRF activation pathway / monoatomic ion transmembrane transport / protein-macromolecule adaptor activity / clathrin-dependent endocytosis of virus by host cell / defense response to virus / molecular adaptor activity / DNA-binding transcription factor binding / entry receptor-mediated virion attachment to host cell / mitochondrial outer membrane / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / positive regulation of canonical NF-kappaB signal transduction / intracellular signal transduction / defense response to bacterium / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / viral translational frameshifting / symbiont-mediated activation of host autophagy / innate immune response / RNA-directed RNA polymerase / serine-type endopeptidase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / protein kinase binding / virion attachment to host cell / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane
Similarity search - Function
IPS1, CARD domain / : / Caspase recruitment domain / Caspase recruitment domain / Thrombin, subunit H - #120 / 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 ...IPS1, CARD domain / : / Caspase recruitment domain / Caspase recruitment domain / Thrombin, subunit H - #120 / 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 core protein, chain A superfamily / : / 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 / NS3 RNA helicase, C-terminal helical domain / 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. / Death-like domain superfamily / 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
Polyprotein / Genome polyprotein / Mitochondrial antiviral-signaling protein
Similarity search - Component
Biological speciesHepatitis C virus subtype 1a
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSchiffer, C.A. / Romano, K.P.
CitationJournal: J.Virol. / Year: 2011
Title: Molecular mechanisms of viral and host cell substrate recognition by hepatitis C virus NS3/4A protease.
Authors: Romano, K.P. / Laine, J.M. / Deveau, L.M. / Cao, H. / Massi, F. / Schiffer, C.A.
History
DepositionMar 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 28, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct.pdbx_descriptor
Revision 1.3Nov 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 1.4Jul 26, 2023Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NS3/4A protease
B: Product MAVS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6325
Polymers22,3742
Non-polymers2583
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-37 kcal/mol
Surface area9890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.096, 58.210, 61.325
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein NS3/4A protease


Mass: 21487.330 Da / Num. of mol.: 1 / Fragment: UNP residues 36-218
Mutation: A1027S, P1028G, I1029D, L1039E, L1040E, I1043Q, I1044E, L1047Q, A1066T, C1073S, C1078L, I1098T, P1112Q, S1165A, C1185S, C1679S, V1686I, I1687N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus subtype 1a / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D6MZ98, UniProt: P27958*PLUS
#2: Protein/peptide Product MAVS


Mass: 886.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q7Z434*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.17 Å3/Da / Density % sol: 43.24 %
Crystal growTemperature: 295 K / Method: hanging drop, vapor diffusion / pH: 6.5
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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorDate: Aug 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 26041 / % possible obs: 99.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.039 / Χ2: 1.013 / Net I/σ(I): 18.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.6-1.663.70.2325661.02999.1
1.66-1.723.70.18225421.01399.1
1.72-1.83.70.14325621.00498.8
1.8-1.93.70.11225641.0199.5
1.9-2.023.70.0925761.01599.5
2.02-2.173.70.07325921.00799.5
2.17-2.393.80.0626091.01199.9
2.39-2.743.80.04826411.001100
2.74-3.453.80.03426561.02199.8
3.45-503.80.02427331.01697.4

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3M5M

3m5m


Resolution: 1.6→27.05 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.2111 / WRfactor Rwork: 0.1871 / Occupancy max: 1 / Occupancy min: 0.08 / FOM work R set: 0.8881 / SU B: 2.949 / SU ML: 0.052 / SU R Cruickshank DPI: 0.0873 / SU Rfree: 0.0833 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1929 1310 5.1 %RANDOM
Rwork0.1714 ---
obs0.1725 25918 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 67.77 Å2 / Biso mean: 28.1905 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20 Å2
2---1.27 Å20 Å2
3---0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.6→27.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1502 0 11 182 1695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221541
X-RAY DIFFRACTIONr_bond_other_d0.0010.021021
X-RAY DIFFRACTIONr_angle_refined_deg1.261.9722097
X-RAY DIFFRACTIONr_angle_other_deg0.8232499
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1875205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00223.39356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65515245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8911512
X-RAY DIFFRACTIONr_chiral_restr0.0730.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211726
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02292
X-RAY DIFFRACTIONr_mcbond_it0.5981.51019
X-RAY DIFFRACTIONr_mcbond_other0.1591.5421
X-RAY DIFFRACTIONr_mcangle_it1.09321639
X-RAY DIFFRACTIONr_scbond_it1.6653522
X-RAY DIFFRACTIONr_scangle_it2.7044.5457
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 88 -
Rwork0.187 1784 -
all-1872 -
obs--98.06 %
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)
15.8636-0.47533.08126.778725.297626.03680.8298-0.25330.0482-0.4681-0.0208-0.81490.1568-0.0797-0.8090.48060.02080.11370.10230.04360.06916.9692-20.8927-2.7105
20.62510.3869-0.52944.2402-0.57830.48560.0560.044-0.0163-0.1615-0.0944-0.1053-0.04350.01240.03830.0467-0.00280.00580.09780.01360.08564.9493-6.123714.882
35.02540.63740.5367.2584-3.17277.93340.1793-0.24490.32410.7052-0.1082-0.0727-0.46370.0495-0.07110.1696-0.01920.01010.0692-0.01890.0825-0.02027.124528.1764
42.21791.3019-1.21094.7614-0.45240.6780.0451-0.2124-0.1175-0.0728-0.0847-0.1264-0.04640.12110.03960.1041-0.0014-0.00080.07950.0210.09737.01223.266916.0661
53.0824-0.89510.02384.94180.13545.6797-0.06920.12810.0156-0.3108-0.1226-0.2835-0.06760.30640.19180.0650.00780.04650.07240.03050.097311.4038-5.35510.9702
611.11712.167-3.38883.81920.62824.82380.0485-0.59880.47780.2431-0.089-0.3516-0.23820.33080.04050.098-0.0431-0.05560.0645-0.0080.12766.325-1.652826.3925
70.81410.73020.81712.61251.16176.12160.11780.095-0.0335-0.1934-0.0113-0.0573-0.0562-0.1954-0.10660.07320.0146-0.00810.07590.00880.0505-0.0377-5.273613.4052
81.9165-0.209-0.00621.6641-0.02010.98130.03450.0061-0.06070.0037-0.0469-0.05520.023-0.03830.01230.04150.0026-0.00050.03920.01170.0534-1.3317-11.346420.2499
94.23962.288-0.98041.6122-1.37562.1335-0.0019-0.1333-0.2531-0.0611-0.1693-0.2040.14060.22630.17120.04620.02430.01120.07290.01730.13728.8388-15.375319.4152
101.47210.8035-0.16091.47760.39361.7022-0.00840.0432-0.12340.0474-0.0544-0.10630.10350.05560.06280.05650.0072-0.01160.03570.01680.0786-0.7902-16.29722.1182
111.5031-0.6686-1.56170.92420.1822.5042-0.0706-0.36950.08810.24250.0490.0295-0.11960.23720.02160.1069-0.02450.00110.2353-0.11030.1042-6.3653-6.79836.0868
123.41922.4444-3.22773.8541-2.5619.4269-0.1569-0.07110.3012-0.1058-0.02520.2488-0.17430.04540.18210.07550.02060.00120.0151-0.0070.1362-8.49311.710124.1857
133.52811.3196-1.13740.5327-0.61141.67370.1733-0.12310.60920.11180.03050.2461-0.2009-0.1947-0.20380.13070.05830.07720.097-0.01840.1767-14.65790.373429.6267
141.93290.6362-1.48562.3112-1.15992.98560.04330.02250.04170.09990.10920.4472-0.1927-0.1717-0.15250.08190.01980.03510.11120.00990.1055-20.0987-6.387328.307
1512.07813.7174-0.14734.2057-2.41555.54950.2763-0.11570.42910.4523-0.3237-0.1152-0.0904-0.25930.04740.1217-0.00890.01450.13770.06640.1335-17.19353.344817.6916
161.7088-0.201-2.2111.1346-0.09662.97650.09660.08170.07040.0066-0.00220.0402-0.1318-0.1082-0.09440.05130.0049-0.00160.04890.00530.1106-8.938-3.275419.4609
172.7104-0.2601-1.20371.28180.7023.17290.0868-0.40140.44510.0597-0.0509-0.0194-0.06-0.0724-0.03590.0776-0.01220.020.1094-0.06830.0903-8.2686-5.120134.0539
187.5145-0.4142-0.25961.2281-0.00970.06050.22460.15570.214-0.0608-0.13550.24310.0023-0.0797-0.08910.0612-0.0014-0.0020.13540.05880.1405-15.9321-7.500320.0591
192.1672-0.55350.46361.8904-1.53682.5436-0.0390.1236-0.02020.14040.19180.3507-0.1819-0.2447-0.15280.07190.00780.0190.10010.03090.0906-17.7332-6.731322.72
2010.1192-2.7629-4.11364.4339-0.63322.7065-0.3535-0.3216-0.41110.11830.09310.07580.29620.04070.26040.1964-0.04820.02670.0838-0.00370.0677-5.6266-18.583431.7254
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A983 - 988
2X-RAY DIFFRACTION2A989 - 997
3X-RAY DIFFRACTION3A998 - 1007
4X-RAY DIFFRACTION4A1008 - 1012
5X-RAY DIFFRACTION5A1013 - 1027
6X-RAY DIFFRACTION6A1028 - 1033
7X-RAY DIFFRACTION7A1034 - 1041
8X-RAY DIFFRACTION8A1042 - 1063
9X-RAY DIFFRACTION9A1064 - 1075
10X-RAY DIFFRACTION10A1076 - 1089
11X-RAY DIFFRACTION11A1090 - 1104
12X-RAY DIFFRACTION12A1105 - 1110
13X-RAY DIFFRACTION13A1111 - 1118
14X-RAY DIFFRACTION14A1119 - 1128
15X-RAY DIFFRACTION15A1129 - 1134
16X-RAY DIFFRACTION16A1135 - 1142
17X-RAY DIFFRACTION17A1143 - 1153
18X-RAY DIFFRACTION18A1154 - 1159
19X-RAY DIFFRACTION19A1160 - 1172
20X-RAY DIFFRACTION20A1173 - 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://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