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- PDB-3rc5: Molecular mechanisms of viral and host-cell substrate recognition... -

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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 / RIG-I binding / positive regulation of hexokinase activity / modulation by virus 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 ...positive regulation of IP-10 production / regulation of peroxisome organization / RIG-I binding / positive regulation of hexokinase activity / modulation by virus 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 / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / viral capsid assembly / protein localization to mitochondrion / positive regulation of response to cytokine stimulus / positive regulation of type I interferon-mediated signaling pathway / adhesion receptor-mediated virion attachment to host cell / TBC/RABGAPs / peroxisomal membrane / hepacivirin / TRAF6 mediated IRF7 activation / negative regulation of type I interferon-mediated signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / cytoplasmic pattern recognition receptor signaling pathway / host cell mitochondrial membrane / negative regulation of viral genome replication / type I interferon-mediated signaling pathway / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / cellular response to exogenous dsRNA / transformation of host cell by virus / positive regulation of cytokinesis / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / TRAF6 mediated NF-kB activation / antiviral innate immune response / host cell membrane / positive regulation of type I interferon production / negative regulation of protein secretion / positive regulation of interferon-alpha production / signaling adaptor activity / ubiquitin ligase complex / positive regulation of defense response to virus by host / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / activation of innate immune response / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / positive regulation of interferon-beta production / serine-type peptidase activity / endoplasmic reticulum-Golgi intermediate compartment membrane / molecular condensate scaffold activity / virion component / positive regulation of interleukin-8 production / Negative regulators of DDX58/IFIH1 signaling / mitochondrial membrane / DDX58/IFIH1-mediated induction of interferon-alpha/beta / PKR-mediated signaling / Evasion by RSV of host interferon responses / kinase binding / positive regulation of DNA-binding transcription factor activity / SH3 domain binding / positive regulation of protein import into nucleus / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / Ovarian tumor domain proteases / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / TRAF3-dependent IRF activation pathway / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / mitochondrial outer membrane / entry receptor-mediated virion attachment to host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / molecular adaptor activity / 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 / RNA helicase / defense response to bacterium / ribonucleoprotein complex / symbiont entry into host cell / induction by virus of host autophagy / positive regulation of protein phosphorylation / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / innate immune response / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / structural molecule activity
Similarity search - Function
IPS1, CARD domain / Caspase recruitment domain / Caspase recruitment domain / 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 ...IPS1, CARD domain / Caspase recruitment domain / Caspase recruitment domain / 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. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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
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.

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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: 2.17 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

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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

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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

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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

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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

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