[English] 日本語
Yorodumi
- PDB-7doc: Crystal structure of Zika NS2B-NS3 protease with compound 5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7doc
TitleCrystal structure of Zika NS2B-NS3 protease with compound 5
Components
  • (Core proteinCapsid) x 4
  • (Genome polyprotein) x 2
  • 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE
  • Serine protease subunit NS2B
KeywordsVIRAL PROTEIN / Viral protease / Protease inhibitor complex
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / GTP binding / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A ...: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / 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 / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.904 Å
AuthorsQuek, J.P.
Funding support Singapore, 3items
OrganizationGrant numberCountry
Other governmentStart up grant Singapore
Other governmentCBRG15May045 Singapore
Other governmentNRF2016NRF-CRP001-063 Singapore
CitationJournal: Acs Med.Chem.Lett. / Year: 2021
Title: 2-Cyanoisonicotinamide Conjugation: A Facile Approach to Generate Potent Peptide Inhibitors of the Zika Virus Protease.
Authors: Patil, N.A. / Quek, J.P. / Schroeder, B. / Morewood, R. / Rademann, J. / Luo, D. / Nitsche, C.
History
DepositionDec 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Core protein
B: Core protein
C: Genome polyprotein
D: Core protein
E: Serine protease subunit NS2B
F: Core protein
G: Core protein
H: Genome polyprotein
I: 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE


Theoretical massNumber of molelcules
Total (without water)83,9419
Polymers83,9419
Non-polymers00
Water6,684371
1
A: Core protein
B: Core protein


Theoretical massNumber of molelcules
Total (without water)20,6902
Polymers20,6902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-26 kcal/mol
Surface area8850 Å2
MethodPISA
2
C: Genome polyprotein
D: Core protein


Theoretical massNumber of molelcules
Total (without water)20,4322
Polymers20,4322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-28 kcal/mol
Surface area8390 Å2
MethodPISA
3
E: Serine protease subunit NS2B
F: Core protein


Theoretical massNumber of molelcules
Total (without water)21,3062
Polymers21,3062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-26 kcal/mol
Surface area9150 Å2
MethodPISA
4
G: Core protein
H: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)20,7182
Polymers20,7182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-27 kcal/mol
Surface area8930 Å2
MethodPISA
5
I: 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE


  • defined by author&software
  • 794 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)7941
Polymers7941
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.154, 59.614, 215.073
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 51 through 61 or (resid 62...
21(chain C and (resid 51 through 65 or (resid 66...
31(chain E and (resid 51 through 61 or (resid 62...
41(chain G and (resid 51 through 61 or (resid 62...
12(chain B and (resid 18 through 29 or (resid 30...
22(chain D and (resid 18 through 30 or resid 34...
32(chain F and (resid 18 through 60 or (resid 64...
42(chain H and (resid 18 through 30 or resid 34...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 51 through 61 or (resid 62...A51 - 61
121(chain A and (resid 51 through 61 or (resid 62...A62 - 66
131(chain A and (resid 51 through 61 or (resid 62...A50 - 88
141(chain A and (resid 51 through 61 or (resid 62...A50 - 88
151(chain A and (resid 51 through 61 or (resid 62...A50 - 88
161(chain A and (resid 51 through 61 or (resid 62...A50 - 88
171(chain A and (resid 51 through 61 or (resid 62...A73
181(chain A and (resid 51 through 61 or (resid 62...A50 - 88
191(chain A and (resid 51 through 61 or (resid 62...A50 - 88
1101(chain A and (resid 51 through 61 or (resid 62...A50 - 88
1111(chain A and (resid 51 through 61 or (resid 62...A50 - 88
211(chain C and (resid 51 through 65 or (resid 66...C51 - 65
221(chain C and (resid 51 through 65 or (resid 66...C66
231(chain C and (resid 51 through 65 or (resid 66...C50 - 87
241(chain C and (resid 51 through 65 or (resid 66...C50 - 87
251(chain C and (resid 51 through 65 or (resid 66...C50 - 87
261(chain C and (resid 51 through 65 or (resid 66...C50 - 87
311(chain E and (resid 51 through 61 or (resid 62...E51 - 61
321(chain E and (resid 51 through 61 or (resid 62...E62 - 66
331(chain E and (resid 51 through 61 or (resid 62...E51 - 89
341(chain E and (resid 51 through 61 or (resid 62...E51 - 89
351(chain E and (resid 51 through 61 or (resid 62...E51 - 89
361(chain E and (resid 51 through 61 or (resid 62...E51 - 89
411(chain G and (resid 51 through 61 or (resid 62...G51 - 61
421(chain G and (resid 51 through 61 or (resid 62...G62 - 66
431(chain G and (resid 51 through 61 or (resid 62...G50 - 88
441(chain G and (resid 51 through 61 or (resid 62...G50 - 88
451(chain G and (resid 51 through 61 or (resid 62...G50 - 88
461(chain G and (resid 51 through 61 or (resid 62...G50 - 88
112(chain B and (resid 18 through 29 or (resid 30...B18 - 29
122(chain B and (resid 18 through 29 or (resid 30...B30
132(chain B and (resid 18 through 29 or (resid 30...B17 - 169
142(chain B and (resid 18 through 29 or (resid 30...B17 - 169
152(chain B and (resid 18 through 29 or (resid 30...B17 - 169
162(chain B and (resid 18 through 29 or (resid 30...B17 - 169
212(chain D and (resid 18 through 30 or resid 34...D18 - 30
222(chain D and (resid 18 through 30 or resid 34...D34 - 53
232(chain D and (resid 18 through 30 or resid 34...D54
242(chain D and (resid 18 through 30 or resid 34...D18 - 169
252(chain D and (resid 18 through 30 or resid 34...D0
262(chain D and (resid 18 through 30 or resid 34...D64 - 65
272(chain D and (resid 18 through 30 or resid 34...D18 - 169
282(chain D and (resid 18 through 30 or resid 34...D18 - 169
292(chain D and (resid 18 through 30 or resid 34...D18 - 169
2102(chain D and (resid 18 through 30 or resid 34...D18 - 169
312(chain F and (resid 18 through 60 or (resid 64...F18 - 60
322(chain F and (resid 18 through 60 or (resid 64...F64 - 65
332(chain F and (resid 18 through 60 or (resid 64...F14 - 171
342(chain F and (resid 18 through 60 or (resid 64...F14 - 171
352(chain F and (resid 18 through 60 or (resid 64...F14 - 171
362(chain F and (resid 18 through 60 or (resid 64...F14 - 171
412(chain H and (resid 18 through 30 or resid 34...H18 - 30
422(chain H and (resid 18 through 30 or resid 34...H34 - 53
432(chain H and (resid 18 through 30 or resid 34...H54
442(chain H and (resid 18 through 30 or resid 34...H18 - 170
452(chain H and (resid 18 through 30 or resid 34...H18 - 170
462(chain H and (resid 18 through 30 or resid 34...H18 - 170
472(chain H and (resid 18 through 30 or resid 34...H18 - 170

NCS ensembles :
ID
1
2

-
Components

-
Protein/peptide , 4 types, 5 molecules AGCEI

#1: Protein/peptide Core protein / Capsid / Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 ...Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 catalytic subunit / Genome polyprotein / Matrix protein / Non-structural protein 1 / Non-structural protein 2A / Non-structural protein 2B / Non-structural protein 3 / Non-structural protein 4A / Non-structural protein 4B / Peptide 2k / Peptide pr / Protein prM / RNA-directed RNA polymerase NS5 / Serine protease NS3 / Serine protease subunit NS2B / Small envelope protein M


Mass: 4347.659 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Gene: GP1, A2G93_72127gpGP1 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2R4LVW1, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#3: Protein/peptide Genome polyprotein


Mass: 4218.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli (E. coli)
References: UniProt: Q32ZE1, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase
#5: Protein/peptide Serine protease subunit NS2B / / Flavivirin protease NS2B regulatory subunit / Non-structural protein 2B


Mass: 4361.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q32ZE1
#8: Protein/peptide 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE


Mass: 793.960 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Protein , 4 types, 4 molecules BDFH

#2: Protein Core protein / Capsid / Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 ...Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 catalytic subunit / Genome polyprotein / Matrix protein / Non-structural protein 1 / Non-structural protein 2A / Non-structural protein 2B / Non-structural protein 3 / Non-structural protein 4A / Non-structural protein 4B / Peptide 2k / Peptide pr / Protein prM / RNA-directed RNA polymerase NS5 / Serine protease NS3 / Serine protease subunit NS2B / Small envelope protein M


Mass: 16342.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Gene: GP1, A2G93_63394gpGP1 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A142IX72, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#4: Protein Core protein / Capsid / Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 ...Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 catalytic subunit / Genome polyprotein / Matrix protein / Non-structural protein 1 / Non-structural protein 2A / Non-structural protein 2B / Non-structural protein 3 / Non-structural protein 4A / Non-structural protein 4B / Peptide 2k / Peptide pr / Protein prM / RNA-directed RNA polymerase NS5 / Serine protease NS3 / Serine protease subunit NS2B / Small envelope protein M


Mass: 16213.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Gene: GP1, A2G93_63394gpGP1 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A142IX72, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#6: Protein Core protein / Capsid / Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 ...Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 catalytic subunit / Genome polyprotein / Matrix protein / Non-structural protein 1 / Non-structural protein 2A / Non-structural protein 2B / Non-structural protein 3 / Non-structural protein 4A / Non-structural protein 4B / Peptide 2k / Peptide pr / Protein prM / RNA-directed RNA polymerase NS5 / Serine protease NS3 / Serine protease subunit NS2B / Small envelope protein M


Mass: 16944.318 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Gene: GP1, A2G93_63394gpGP1 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A142IX72, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#7: Protein Genome polyprotein / NS3 Protease


Mass: 16370.678 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli (E. coli) / References: UniProt: H8XX12

-
Non-polymers , 1 types, 371 molecules

#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium Sulfate, 0.1M Sodium Acetate Trihydrate pH 4.6, 30% Peg 2000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.15
ReflectionResolution: 1.904→45.63 Å / Num. obs: 60261 / % possible obs: 99.39 % / Redundancy: 13.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1312 / Rpim(I) all: 0.03716 / Rrim(I) all: 0.1365 / Net I/σ(I): 12.2
Reflection shellResolution: 1.904→1.972 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.8121 / Num. unique obs: 5640 / CC1/2: 0.925 / Rpim(I) all: 0.2344 / Rrim(I) all: 0.8459 / % possible all: 94.08

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GPI

5gpi


Resolution: 1.904→45.63 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2286 2981 4.97 %
Rwork0.2092 57210 -
obs-60243 99.4 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.19 Å2 / Biso mean: 45.9095 Å2 / Biso min: 23.6 Å2
Refinement stepCycle: final / Resolution: 1.904→45.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5501 0 104 371 5976
Biso mean--73.4 50.76 -
Num. residues----765
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A436X-RAY DIFFRACTION3.48TORSIONAL
12C436X-RAY DIFFRACTION3.48TORSIONAL
13E436X-RAY DIFFRACTION3.48TORSIONAL
14G436X-RAY DIFFRACTION3.48TORSIONAL
21B1720X-RAY DIFFRACTION3.48TORSIONAL
22D1720X-RAY DIFFRACTION3.48TORSIONAL
23F1720X-RAY DIFFRACTION3.48TORSIONAL
24H1720X-RAY DIFFRACTION3.48TORSIONAL
LS refinement shellResolution: 1.904→1.972 Å / Rfactor Rfree error: 0 /
RfactorNum. reflection
Rfree0.275 281
Rwork0.2947 5630
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)
15.33740.96372.74063.0533-1.10522.30530.0897-0.76831.0930.8508-0.08550.9012-0.6763-0.3187-0.08830.58330.08780.14340.6624-0.04730.3915-8.9807-0.538240.233
23.7946-2.14351.59637.6238-2.17790.92370.14890.3016-0.09960.8049-0.4879-0.6483-1.1144-0.21780.23370.73220.026-0.0630.51520.03170.29711.7774-5.277150.4588
33.6973-0.41364.7570.0983-0.36716.57040.0546-1.33490.09221.7733-0.37720.3565-0.13150.36820.14691.3447-0.0182-0.02890.73910.04660.21151.4756-18.134459.323
46.0150.58951.41958.8221-0.89880.45570.19740.1550.18920.7228-0.01520.6331-0.12281.0276-0.29191.0056-0.0817-0.00850.73050.13290.3013-4.6179-33.63950.0877
53.3549-1.05291.83141.6975-1.70822.7236-0.22940.0424-0.3494-0.71670.2193-0.00880.47690.05060.05960.646-0.15990.05860.7348-0.02440.229-9.8242-30.357935.3695
65.5518-0.3859-0.81311.57-1.04733.0567-0.25180.16250.67230.10730.26370.1479-0.6161-0.1985-0.10960.55760.04750.01470.5499-0.06590.2253-6.6541-4.410643.4568
73.54020.3518-0.75141.86070.0872.9665-0.27490.0105-0.1382-0.11680.180.1283-0.2931-0.18710.13480.5304-0.02430.03540.5252-0.03130.1237-2.6572-10.77736.9924
81.9714-1.92580.79056.5808-0.16563.8495-0.09520.15190.0917-0.56110.27940.4977-0.841-0.2364-0.23520.54590.00440.01270.620.06630.2817-3.0755-5.226732.3258
92.8312.3718-0.7286.87081.49552.7543-0.0881-0.5368-0.1624-0.4656-0.0691-0.5108-0.0188-0.26540.09190.47770.01530.00730.51010.02770.1454-3.2628-15.783933.0385
101.4940.31270.63511.855-1.29523.24630.2002-0.2789-0.19830.6485-0.1363-0.3897-0.35040.5457-0.13140.5499-0.0278-0.04730.6108-0.00070.23266.635-19.522342.9962
110.68931.1998-0.26962.5260.24611.29510.0593-0.2353-0.06971.0951-0.11850.27950.3518-0.0357-0.04470.6643-0.07890.01130.58880.03670.2172-4.7422-20.722849.3484
129.34542.76524.60826.8980.75142.83920.5275-0.5809-0.63750.87720.3807-0.95970.89980.1638-0.79760.7080.0842-0.09650.6088-0.0620.31745.8049-17.017649.4497
131.3165-0.00040.56761.69160.74981.00950.1311-0.15640.2410.1035-0.07930.30380.5208-0.42490.02370.6755-0.00680.0330.66430.05260.1511-6.411-23.611144.5574
144.7986-1.2037-1.00058.52862.08579.07731.315-0.31580.53870.9119-0.4274-1.1377-2.10471.7723-0.21440.8999-0.42970.08820.9360.05210.4483-21.6570.488267.9924
150.15380.480.01382.122-0.92031.58280.13060.8453-0.0939-0.8921-0.3022-0.37380.10150.34970.09660.62550.08540.00160.9918-0.10850.3141-29.2433-17.38652.9269
162.341-1.8516-1.28013.4144-0.07771.3199-0.06740.2288-0.25050.12650.15440.05570.29260.1041-0.13520.58440.1799-0.07080.9354-0.07820.2745-20.9285-28.670372.5636
173.99171.87132.42191.67941.64766.3914-0.5846-0.21260.2614-0.23560.11740.204-0.7599-0.04830.20550.6097-0.01720.01970.63610.13520.1833-27.4291-2.632963.3992
182.0023-1.8366-0.86212.781-0.57693.8823-0.6894-0.63760.80590.2510.3549-0.9212-0.20290.8160.41040.62460.0997-0.05980.88030.0662-0.0537-21.0658-4.667565.4663
193.2554-0.7251-1.10583.15760.65883.6124-0.44580.15720.00470.07060.2395-0.2241-0.55670.870.1840.4312-0.03190.01920.57110.00330.1517-28.484-9.696970.8864
201.8321-0.1719-0.93064.74840.84680.8721-0.221-0.02010.453-0.12180.4143-0.7654-0.59920.2892-0.24630.5786-0.1122-0.0270.7089-0.02040.1914-28.4748-4.248175.5968
211.9554-1.85360.81066.3052-1.20892.845-0.09860.0561-0.0906-0.15170.40710.16280.19560.4221-0.41750.46170.02750.02490.5445-0.00390.1545-28.1355-14.716874.8488
221.7561-0.16360.4966.17594.22324.9039-0.13150.3509-0.20330.13710.02920.1490.2528-0.1786-0.00770.4618-0.01430.00410.6128-0.02870.1878-37.4005-18.3164.6663
231.21540.4908-0.47412.91240.76750.5466-0.12590.2822-0.0163-0.64530.1896-0.1953-0.08690.116-0.06230.55670.10440.0590.7565-0.03910.2346-26.3259-18.846156.4561
242.03390.07790.21792.4123-0.74781.75380.23030.336-0.4533-0.1788-0.1562-0.07680.13760.676-0.01140.56750.04760.02320.7724-0.070.1836-25.9751-20.976362.2831
255.78162.3233-0.71158.89093.27188.81680.32480.51280.6372-0.28440.48240.6661-0.5479-1.4217-0.37280.3445-0.04490.01640.85570.23140.4123-15.1058-9.35310.9148
265.8241-1.70724.14165.24790.72274.09920.31960.4165-0.0945-1.63930.0558-0.06880.2110.2097-0.22930.4001-0.0519-0.02310.55660.09210.2165-8.4859-18.68982.0703
274.95033.597-2.35873.0428-1.4071.5889-0.59320.99890.727-1.59850.38870.3535-0.0119-0.1123-0.00890.57320.0134-0.02750.77080.04560.33513.9246-15.3502-5.6298
285.3391-1.8502-0.918.61153.99828.26150.22530.116-0.06990.2194-0.2984-1.241-0.43180.20420.16860.4325-0.02950.03390.610.17820.42618.0673-8.3016.2523
292.7871-1.9563-0.3671.61210.32020.06890.3198-0.80310.11270.6545-0.224-0.0286-0.27820.40620.12620.7286-0.2175-0.03120.61430.01640.221510.915-4.876220.9767
303.1427-1.3826-0.50049.59462.89259.22650.0557-0.19140.7998-0.20160.7061-1.299-0.23611.2679-0.72010.5388-0.11620.05830.5701-0.07250.425418.4245-1.751314.0336
310.92582.0774-0.59339.6378-1.17920.38330.02440.59930.127-0.0199-0.02231.03640.04960.03810.10040.4040.0436-0.02180.61620.06050.3017-14.4653-19.2089.9103
322.54160.09312.06898.9896-1.81142.06610.0747-0.01390.58670.4551-0.65150.4931-0.0992-0.49460.48660.44340.0030.07930.704-0.02820.1113-10.1815-7.572911.7064
332.16160.4737-1.59051.8193-0.23112.22360.1613-0.01470.05560.2958-0.12130.1495-0.0466-0.1871-0.04230.4159-0.0173-0.00660.43470.0220.1343-2.9088-15.352617.2889
342.83511.776-0.77542.6155-0.7160.2997-0.07340.039-0.043-0.04750.0535-0.0548-0.00480.06090.03130.3422-0.00350.00440.44340.0420.14734.8536-11.4416.2804
354.103-0.47930.13892.15261.84682.7070.14090.07430.0216-0.2815-0.05110.4847-0.0166-0.5983-0.04020.3743-0.036-0.01990.45370.09080.2285-38.1364-40.21987.7478
363.1521.78250.10534.38971.790.8676-0.73311.91210.1342-1.9580.41550.44260.0725-0.35280.34220.78290.07360.0290.77920.00560.1951-21.8131-46.4875-4.9393
372.00160.73289.63425.61683.16842.0009-0.6827-0.22190.6665-0.2101-0.5789-0.1096-0.1988-0.17130.40170.4233-0.10420.07330.6111-0.04610.1829-7.4858-38.88785.1926
380.1213-0.43170.62763.3279-1.86083.31130.3921-0.80360.01570.361-0.4047-0.1953-0.14780.9015-0.00040.5779-0.1543-0.01210.57560.00840.1973-10.6369-34.703819.551
393.38432.522-0.36356.52263.47193.69580.0665-0.08810.37110.6362-0.18750.98860.5308-0.39060.07660.3678-0.0121-0.02790.52660.05540.21-37.4168-40.74888.4523
403.93282.11592.14581.6702-0.02633.8062-0.19650.42050.9796-0.2308-0.04380.7043-0.3276-0.64910.27460.3990.00150.02070.55460.04220.2927-35.6227-34.9399.8334
413.00391.9077-0.50922.7497-0.06473.2744-0.0714-0.06230.41440.43110.1560.35570.0312-0.3469-0.0590.39560.02160.03140.49240.03550.1678-34.5936-41.259818.6748
424.09390.1447-2.20560.76180.12681.8508-0.03580.0634-0.3543-0.0274-0.1288-0.03960.2882-0.11540.11380.4001-0.0041-0.01740.38390.0390.1474-23.0642-47.525514.6457
432.95390.9783-1.05342.658-0.08030.3816-0.04720.1792-0.0403-0.08930.0742-0.01440.1014-0.0106-0.01730.36530.0046-0.00030.40130.02030.1132-19.9532-41.51696.0436
442.4499-0.46561.32912.46041.86112.56390.0244-0.3090.1761-0.42880.0454-0.3269-0.01440.2209-0.00730.36850.13170.06930.54190.02190.2183-16.7266-38.896910.6895
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 50 through 54 )A50 - 54
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 59 )A55 - 59
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 69 )A60 - 69
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 74 )A70 - 74
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 88 )A75 - 88
6X-RAY DIFFRACTION6chain 'B' and (resid 17 through 42 )B17 - 42
7X-RAY DIFFRACTION7chain 'B' and (resid 43 through 53 )B43 - 53
8X-RAY DIFFRACTION8chain 'B' and (resid 54 through 71 )B54 - 71
9X-RAY DIFFRACTION9chain 'B' and (resid 72 through 79 )B72 - 79
10X-RAY DIFFRACTION10chain 'B' and (resid 80 through 94 )B80 - 94
11X-RAY DIFFRACTION11chain 'B' and (resid 95 through 136 )B95 - 136
12X-RAY DIFFRACTION12chain 'B' and (resid 137 through 145 )B137 - 145
13X-RAY DIFFRACTION13chain 'B' and (resid 146 through 169 )B146 - 169
14X-RAY DIFFRACTION14chain 'C' and (resid 50 through 54 )C50 - 54
15X-RAY DIFFRACTION15chain 'C' and (resid 55 through 74 )C55 - 74
16X-RAY DIFFRACTION16chain 'C' and (resid 75 through 87 )C75 - 87
17X-RAY DIFFRACTION17chain 'D' and (resid 18 through 27 )D18 - 27
18X-RAY DIFFRACTION18chain 'D' and (resid 28 through 42 )D28 - 42
19X-RAY DIFFRACTION19chain 'D' and (resid 43 through 53 )D43 - 53
20X-RAY DIFFRACTION20chain 'D' and (resid 54 through 71 )D54 - 71
21X-RAY DIFFRACTION21chain 'D' and (resid 72 through 79 )D72 - 79
22X-RAY DIFFRACTION22chain 'D' and (resid 80 through 94 )D80 - 94
23X-RAY DIFFRACTION23chain 'D' and (resid 95 through 118 )D95 - 118
24X-RAY DIFFRACTION24chain 'D' and (resid 119 through 169 )D119 - 169
25X-RAY DIFFRACTION25chain 'E' and (resid 51 through 55 )E51 - 55
26X-RAY DIFFRACTION26chain 'E' and (resid 56 through 60 )E56 - 60
27X-RAY DIFFRACTION27chain 'E' and (resid 61 through 70 )E61 - 70
28X-RAY DIFFRACTION28chain 'E' and (resid 71 through 75 )E71 - 75
29X-RAY DIFFRACTION29chain 'E' and (resid 76 through 83 )E76 - 83
30X-RAY DIFFRACTION30chain 'E' and (resid 84 through 89 )E84 - 89
31X-RAY DIFFRACTION31chain 'F' and (resid 14 through 26 )F14 - 26
32X-RAY DIFFRACTION32chain 'F' and (resid 27 through 42 )F27 - 42
33X-RAY DIFFRACTION33chain 'F' and (resid 43 through 94 )F43 - 94
34X-RAY DIFFRACTION34chain 'F' and (resid 95 through 171 )F95 - 171
35X-RAY DIFFRACTION35chain 'G' and (resid 50 through 59 )G50 - 59
36X-RAY DIFFRACTION36chain 'G' and (resid 60 through 69 )G60 - 69
37X-RAY DIFFRACTION37chain 'G' and (resid 70 through 74 )G70 - 74
38X-RAY DIFFRACTION38chain 'G' and (resid 75 through 88 )G75 - 88
39X-RAY DIFFRACTION39chain 'H' and (resid 18 through 28 )H18 - 28
40X-RAY DIFFRACTION40chain 'H' and (resid 29 through 42 )H29 - 42
41X-RAY DIFFRACTION41chain 'H' and (resid 43 through 71 )H43 - 71
42X-RAY DIFFRACTION42chain 'H' and (resid 72 through 94 )H72 - 94
43X-RAY DIFFRACTION43chain 'H' and (resid 95 through 155 )H95 - 155
44X-RAY DIFFRACTION44chain 'H' and (resid 156 through 170 )H156 - 170

+
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