[English] 日本語
Yorodumi
- PDB-5lex: Native human 20S proteasome in Mg-Acetate at 2.2 Angstrom -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lex
TitleNative human 20S proteasome in Mg-Acetate at 2.2 Angstrom
Components
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
KeywordsHYDROLASE / Proteasome / Multicatalytic Proteinase / NTN-Hydrolase
Function / homology
Function and homology information


purine ribonucleoside triphosphate binding / Antigen processing: Ub, ATP-independent proteasomal degradation / sperm glycocalyx / Regulation of ornithine decarboxylase (ODC) / perinuclear theca / Proteasome assembly / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / myofibril ...purine ribonucleoside triphosphate binding / Antigen processing: Ub, ATP-independent proteasomal degradation / sperm glycocalyx / Regulation of ornithine decarboxylase (ODC) / perinuclear theca / Proteasome assembly / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / myofibril / proteasomal ubiquitin-independent protein catabolic process / sperm head-tail coupling apparatus / immune system process / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome assembly / proteasome core complex, alpha-subunit complex / ciliary tip / : / proteasome complex / sarcomere / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / sperm end piece / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / centriole / negative regulation of inflammatory response to antigenic stimulus / P-body / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Degradation of DVL / lipopolysaccharide binding / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of CRY and PER proteins / Degradation of AXIN / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / G2/M Checkpoints / Hedgehog ligand biogenesis / Degradation of GLI1 by the proteasome / Defective CFTR causes cystic fibrosis / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of RUNX3 expression and activity / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / Hedgehog 'on' state / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Vif-mediated degradation of APOBEC3G / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / Degradation of CDH1 / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / ABC-family proteins mediated transport / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / response to virus / Regulation of expression of SLITs and ROBOs / nuclear matrix / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / KEAP1-NFE2L2 pathway / UCH proteinases / Downstream TCR signaling / peptidase activity / Antigen processing: Ubiquitination & Proteasome degradation / sperm principal piece / RUNX1 regulates transcription of genes involved in differentiation of HSCs / ER-Phagosome pathway / Neddylation / regulation of inflammatory response / response to oxidative stress / sperm midpiece / secretory granule lumen / endopeptidase activity / ficolin-1-rich granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / Ub-specific processing proteases / cilium / nuclear body
Similarity search - Function
Proteasome subunit alpha 1 / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha5 / Proteasome subunit alpha6 ...Proteasome subunit alpha 1 / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha5 / Proteasome subunit alpha6 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Proteasome subunit alpha type-7 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-4 / Proteasome subunit beta type-6 ...: / Proteasome subunit alpha type-7 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-4 / Proteasome subunit beta type-6 / Proteasome subunit beta type-5 / Proteasome subunit beta type-3 / Proteasome subunit beta type-2 / Proteasome subunit alpha type-6 / Proteasome subunit beta type-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsSchrader, J. / Henneberg, F. / Mata, R. / Tittmann, K. / Schneider, T.R. / Stark, H. / Bourenkov, G. / Chari, A.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research FoundationCH1098/1-1 Germany
German Research FoundationSFB860-TP A5 Germany
Bundesministerium fuer Bildung und Forschung05K2013-624 Germany
CitationJournal: Science / Year: 2016
Title: The inhibition mechanism of human 20S proteasomes enables next-generation inhibitor design.
Authors: Schrader, J. / Henneberg, F. / Mata, R.A. / Tittmann, K. / Schneider, T.R. / Stark, H. / Bourenkov, G. / Chari, A.
History
DepositionJun 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proteasome subunit alpha type-2
B: Proteasome subunit alpha type-4
C: Proteasome subunit alpha type-7
D: Proteasome subunit alpha type-5
E: Proteasome subunit alpha type-1
F: Proteasome subunit alpha type-3
G: Proteasome subunit alpha type-6
H: Proteasome subunit beta type-7
I: Proteasome subunit beta type-3
J: Proteasome subunit beta type-2
K: Proteasome subunit beta type-5
L: Proteasome subunit beta type-1
M: Proteasome subunit beta type-4
N: Proteasome subunit beta type-6
O: Proteasome subunit alpha type-2
P: Proteasome subunit alpha type-4
Q: Proteasome subunit alpha type-7
R: Proteasome subunit alpha type-5
S: Proteasome subunit alpha type-1
T: Proteasome subunit alpha type-3
U: Proteasome subunit alpha type-6
V: Proteasome subunit beta type-7
W: Proteasome subunit beta type-3
X: Proteasome subunit beta type-2
Y: Proteasome subunit beta type-5
Z: Proteasome subunit beta type-1
a: Proteasome subunit beta type-4
b: Proteasome subunit beta type-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)721,57852
Polymers718,98128
Non-polymers2,59824
Water60,0083331
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area116590 Å2
ΔGint-486 kcal/mol
Surface area212650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.860, 203.150, 316.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21O
12B
22P
13C
23Q
14D
24R
15E
25S
16F
26T
17G
27U
18H
28V
19I
29W
110J
210X
111K
211Y
112L
212Z
113M
213a
114N
214b

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGILEILEAA3 - 2324 - 233
21ARGARGILEILEOO3 - 2324 - 233
12SERSERALAALABB2 - 2472 - 247
22SERSERALAALAPP2 - 2472 - 247
13SERSERGLUGLUCC2 - 2372 - 237
23SERSERGLUGLUQQ2 - 2372 - 237
14ASPASPILEILEDD9 - 2419 - 241
24ASPASPILEILERR9 - 2419 - 241
15ASNASNLEULEUEE4 - 2364 - 236
25ASNASNLEULEUSS4 - 2364 - 236
16GLYGLYLEULEUFF6 - 2437 - 244
26GLYGLYLEULEUTT6 - 2437 - 244
17SERSERARGARGGG2 - 2452 - 245
27SERSERARGARGUU2 - 2452 - 245
18THRTHRGLUGLUHH1 - 2201 - 220
28THRTHRGLUGLUVV1 - 2201 - 220
19SERSERASPASPII1 - 2042 - 205
29SERSERASPASPWW1 - 2042 - 205
110METMETPHEPHEJJ1 - 1961 - 196
210METMETPHEPHEXX1 - 1961 - 196
111THRTHRTYRTYRKK1 - 1991 - 199
211THRTHRTYRTYRYY1 - 1991 - 199
112ARGARGASPASPLL1 - 2131 - 213
212ARGARGASPASPZZ1 - 2131 - 213
113THRTHRSERSERMM1 - 2161 - 216
213THRTHRSERSERaAA1 - 2161 - 216
114THRTHRTHRTHRNN1 - 2011 - 201
214THRTHRTHRTHRbBA1 - 2011 - 201

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14

-
Components

-
Proteasome subunit alpha type- ... , 7 types, 14 molecules AOBPCQDRESFTGU

#1: Protein Proteasome subunit alpha type-2 / Macropain subunit C3 / Multicatalytic endopeptidase complex subunit C3 / Proteasome component C3


Mass: 25927.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P25787, proteasome endopeptidase complex
#2: Protein Proteasome subunit alpha type-4 / Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / ...Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / Proteasome subunit L


Mass: 29525.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P25789, proteasome endopeptidase complex
#3: Protein Proteasome subunit alpha type-7 / Proteasome subunit RC6-1 / Proteasome subunit XAPC7


Mass: 27986.941 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: O14818, proteasome endopeptidase complex
#4: Protein Proteasome subunit alpha type-5 / Macropain zeta chain / Multicatalytic endopeptidase complex zeta chain / Proteasome zeta chain


Mass: 26435.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P28066, proteasome endopeptidase complex
#5: Protein Proteasome subunit alpha type-1 / 30 kDa prosomal protein / PROS-30 / Macropain subunit C2 / Multicatalytic endopeptidase complex ...30 kDa prosomal protein / PROS-30 / Macropain subunit C2 / Multicatalytic endopeptidase complex subunit C2 / Proteasome component C2 / Proteasome nu chain


Mass: 29720.752 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P25786, proteasome endopeptidase complex
#6: Protein Proteasome subunit alpha type-3 / Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8


Mass: 28469.252 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P25788, proteasome endopeptidase complex
#7: Protein Proteasome subunit alpha type-6 / 27 kDa prosomal protein / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota ...27 kDa prosomal protein / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota chain / Proteasome iota chain


Mass: 27739.760 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P60900, proteasome endopeptidase complex

-
Proteasome subunit beta type- ... , 7 types, 14 molecules HVIWJXKYLZMaNb

#8: Protein Proteasome subunit beta type-7 / Macropain chain Z / Multicatalytic endopeptidase complex chain Z / Proteasome subunit Z


Mass: 25321.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: Q99436, proteasome endopeptidase complex
#9: Protein Proteasome subunit beta type-3 / Proteasome chain 13 / Proteasome component C10-II / Proteasome theta chain


Mass: 22972.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P49720, proteasome endopeptidase complex
#10: Protein Proteasome subunit beta type-2 / Macropain subunit C7-I / Multicatalytic endopeptidase complex subunit C7-I / Proteasome component C7-I


Mass: 22989.402 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P49721, proteasome endopeptidase complex
#11: Protein Proteasome subunit beta type-5 / Macropain epsilon chain / Multicatalytic endopeptidase complex epsilon chain / Proteasome chain 6 / ...Macropain epsilon chain / Multicatalytic endopeptidase complex epsilon chain / Proteasome chain 6 / Proteasome epsilon chain / Proteasome subunit MB1 / Proteasome subunit X


Mass: 22484.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P28074, proteasome endopeptidase complex
#12: Protein Proteasome subunit beta type-1 / Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / ...Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Proteasome gamma chain


Mass: 23578.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P20618, proteasome endopeptidase complex
#13: Protein Proteasome subunit beta type-4 / 26 kDa prosomal protein / PROS-26 / Macropain beta chain / Multicatalytic endopeptidase complex ...26 kDa prosomal protein / PROS-26 / Macropain beta chain / Multicatalytic endopeptidase complex beta chain / Proteasome beta chain / Proteasome chain 3 / HsN3


Mass: 24414.740 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P28070, proteasome endopeptidase complex
#14: Protein Proteasome subunit beta type-6 / Macropain delta chain / Multicatalytic endopeptidase complex delta chain / Proteasome delta chain / ...Macropain delta chain / Multicatalytic endopeptidase complex delta chain / Proteasome delta chain / Proteasome subunit Y


Mass: 21921.836 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P28072, proteasome endopeptidase complex

-
Non-polymers , 4 types, 3355 molecules

#15: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#16: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#17: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3331 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris, 0.2 M Magnesium Chloride, 10 % PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 9, 2015 / Details: CRL Transfocator
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.2→170.89 Å / Num. obs: 346869 / % possible obs: 98.81 % / Redundancy: 6.9 % / CC1/2: 1 / Net I/σ(I): 13
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 0.9 / CC1/2: 0.36 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5LE5

5le5


Resolution: 2.2→170.89 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 17.074 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.192 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2214 18235 5 %RANDOM
Rwork0.17702 ---
obs0.17922 346869 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 65.884 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å2-0 Å2-0 Å2
2---1.71 Å20 Å2
3---1.37 Å2
Refinement stepCycle: LAST / Resolution: 2.2→170.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47812 0 159 3331 51302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01949272
X-RAY DIFFRACTIONr_bond_other_d0.0050.0246824
X-RAY DIFFRACTIONr_angle_refined_deg1.7551.96866674
X-RAY DIFFRACTIONr_angle_other_deg1.3033107478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.25356301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46923.7112126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72158272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.87115340
X-RAY DIFFRACTIONr_chiral_restr0.1030.27527
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0256098
X-RAY DIFFRACTIONr_gen_planes_other0.0050.0211190
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_it1.3572.88125031
X-RAY DIFFRACTIONr_mcbond_other1.3572.8825030
X-RAY DIFFRACTIONr_mcangle_it2.1784.31531271
X-RAY DIFFRACTIONr_mcangle_other2.1784.31531272
X-RAY DIFFRACTIONr_scbond_it2.2283.13724241
X-RAY DIFFRACTIONr_scbond_other2.2283.13724241
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1034.60135364
X-RAY DIFFRACTIONr_long_range_B_refined8.68424.52656167
X-RAY DIFFRACTIONr_long_range_B_other8.68424.52756168
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A259000.07
12O259000.07
21B275200.08
22P275200.08
31C250000.1
32Q250000.1
41D263160.08
42R263160.08
51E273820.08
52S273820.08
61F279240.08
62T279240.08
71G264080.08
72U264080.08
81H247340.06
82V247340.06
91I256200.07
92W256200.07
101J244640.08
102X244640.08
111K227720.08
112Y227720.08
121L245760.06
122Z245760.06
131M249900.08
132a249900.08
141N230180.06
142b230180.06
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 1232 -
Rwork0.363 24436 -
obs--94.56 %
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)
11.7810.35350.59072.40720.07752.176-0.05550.1110.1032-0.2714-0.0571-0.50420.10350.69190.11260.51120.16620.14680.42880.0730.142477.0843206.7320.9956
21.00360.0208-0.01162.4241-0.29911.5115-0.05780.2084-0.2637-0.3428-0.0302-0.42150.42490.46580.08810.89270.21780.08660.2941-0.03380.153865.0834177.7716-0.0344
32.33180.21130.34552.9827-0.19862.21180.0628-0.0121-0.7923-0.34740.0562-0.01610.7071-0.0166-0.1191.0258-0.0779-0.14570.2403-0.02990.328634.3931169.8054-3.9316
40.7639-0.139-1.23261.4654-0.13172.2436-0.09040.2415-0.2175-0.33550.00990.27270.436-0.54380.08050.8693-0.1627-0.34470.4850.04030.351510.4927188.3891-8.1497
51.9307-0.2896-0.1011.13860.0011.5590.05440.1739-0.3149-0.1682-0.01330.32270.2711-0.553-0.0410.5172-0.0798-0.17510.35110.03670.16789.831219.904-9
61.8146-0.5437-0.15272.1792-0.14521.3130.06610.13560.2871-0.1823-0.06060.2314-0.1197-0.1615-0.00550.42410.0079-0.08260.17010.0440.113232.394240.101-7.584
71.0225-0.1160.19253.07410.70621.84460.05140.29570.2925-0.4299-0.1058-0.3133-0.24260.43470.05440.41820.00580.06820.32250.14490.122964.017233.587-3.672
80.3957-0.131-0.0041.9633-0.38971.06090.0071-0.0219-0.1302-0.0515-0.1466-0.19610.0290.5060.13950.2202-0.02410.04540.37540.08210.090871.352213.93239.439
90.57570.26140.62111.5384-0.72281.82210.04620.0258-0.0632-0.1862-0.1976-0.16760.23760.54590.15140.39060.15040.06230.35010.11840.052466.571186.51839.549
101.13350.4573-0.19771.1544-0.42113.1452-0.08240.0727-0.1074-0.3466-0.01960.24260.7102-0.11310.1020.67590.0075-0.0460.05590.0020.126939.129170.26536.27
111.4462-0.155-0.8011.83370.20332.1907-0.04890.0876-0.0819-0.28530.07760.30990.5327-0.5189-0.02870.5174-0.2504-0.23730.33780.1190.32858.034180.78332.228
120.81320.2142-0.39391.46140.4521.16780.0188-0.03650.0409-0.20130.02450.4787-0.0018-0.658-0.04330.3331-0.0885-0.17390.62880.19710.344-1.575210.26930.853
130.95090.31830.17441.450.39392.4805-0.0114-0.0290.16540.02770.11880.2817-0.4705-0.4209-0.10750.34530.0995-0.01460.23970.08670.152816.302237.92133.116
141.6756-0.47080.25681.3404-0.52572.33170.0365-0.01420.1085-0.0287-0.07390.0087-0.4690.14650.03740.3872-0.09810.00720.0860.01550.017148.774241.43535.653
151.4581-0.03910.64291.9862-0.05092.4114-0.0565-0.12530.31090.1155-0.00220.6356-0.517-0.6580.05880.51720.24680.26870.720.06760.5342-7.241225.984103.023
160.98250.29660.4521.64230.52371.8666-0.0415-0.2949-0.02620.27160.0110.68070.0238-0.95580.03050.3825-0.04790.23690.84950.17990.5451-7.9185194.6927104.7118
172.94080.47990.36462.34340.35872.67720.1762-0.0812-0.83160.2065-0.02430.43030.7164-0.5201-0.15190.5847-0.11740.08120.43380.13120.504315.6549174.6044109.5298
180.79550.0761-0.45891.3741-0.03252.3188-0.0875-0.1702-0.31920.17720.0210.1820.4320.07140.06650.4505-0.00520.07970.30.10220.175545.8082181.4691113.0041
191.9064-0.1618-0.13761.5492-0.08051.7961-0.075-0.3763-0.16290.3556-0.0175-0.2165-0.07630.54020.09250.442-0.1268-0.00510.40250.04330.056258.8742210.1019113.9881
202.61250.7301-0.89872.419-0.01461.51330.2389-0.5160.15440.2172-0.1188-0.2095-0.70740.3516-0.12010.82-0.12620.11480.2636-0.0680.067646.9821237.7836111.7206
211.70750.5121-0.00711.6044-0.17871.3133-0.0816-0.27680.47110.25290.00740.2392-0.6611-0.17190.07420.86450.21790.18970.3789-0.05450.345416.3412244.7599107.3743
220.97480.50980.0371.5326-0.13171.0229-0.0034-0.0167-0.00570.04870.14440.3475-0.255-0.5906-0.14090.37070.1880.12720.49870.10090.33911.3419230.459365.1491
230.90470.23180.74951.03430.56162.41970.0214-0.03610.0335-0.00330.1230.3982-0.165-0.8619-0.14440.2192-0.02790.03560.6940.22040.465-6.1114202.99465.231
241.005-0.3008-0.33931.27370.09692.3348-0.0387-0.0801-0.16330.00860.1120.19230.492-0.2994-0.07330.3802-0.2091-0.0360.2880.0960.322611.7048176.645368.5433
251.54790.3319-0.81641.75490.08912.4947-0.0762-0.20420.00010.069-0.00430.02650.60390.15270.08040.39740.04560.00890.1240.04680.087944.1342172.992172.9427
260.8244-0.0934-0.54911.5862-0.31221.6630.0264-0.0588-0.03750.0691-0.2015-0.20520.13870.59060.17510.19810.00680.02760.35410.08790.049565.6909195.761873.9198
270.8281-0.1237-0.06421.7146-0.71882.36570.0208-0.02390.12320.1748-0.1078-0.1005-0.48660.47230.0870.3349-0.17120.0090.22350.00790.027260.6985228.466670.989
281.885-0.08590.21761.3525-0.14042.13060.0195-0.02590.1430.1844-0.0260.1485-0.5851-0.07110.00650.56280.04260.06040.0867-0.03050.071632.8628245.645767.994
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 232
2X-RAY DIFFRACTION2B2 - 249
3X-RAY DIFFRACTION3C2 - 238
4X-RAY DIFFRACTION4D9 - 241
5X-RAY DIFFRACTION5E4 - 237
6X-RAY DIFFRACTION6F6 - 244
7X-RAY DIFFRACTION7G2 - 245
8X-RAY DIFFRACTION8H1 - 220
9X-RAY DIFFRACTION9I1 - 204
10X-RAY DIFFRACTION10J1 - 196
11X-RAY DIFFRACTION11K1 - 201
12X-RAY DIFFRACTION12L1 - 213
13X-RAY DIFFRACTION13M1 - 216
14X-RAY DIFFRACTION14N1 - 202
15X-RAY DIFFRACTION15O3 - 232
16X-RAY DIFFRACTION16P2 - 248
17X-RAY DIFFRACTION17Q2 - 240
18X-RAY DIFFRACTION18R9 - 241
19X-RAY DIFFRACTION19S2 - 239
20X-RAY DIFFRACTION20T5 - 244
21X-RAY DIFFRACTION21U2 - 245
22X-RAY DIFFRACTION22V1 - 220
23X-RAY DIFFRACTION23W1 - 204
24X-RAY DIFFRACTION24X1 - 196
25X-RAY DIFFRACTION25Y1 - 199
26X-RAY DIFFRACTION26Z1 - 213
27X-RAY DIFFRACTION27a1 - 216
28X-RAY DIFFRACTION28b1 - 203

+
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