[English] 日本語
Yorodumi
- PDB-4y8j: Yeast 20S proteasome in complex with Ac-LLL-ep -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4y8j
TitleYeast 20S proteasome in complex with Ac-LLL-ep
Components
  • (Proteasome subunit alpha type- ...) x 6
  • (Proteasome subunit beta type- ...) x 7
  • Ac-PLL-ep
  • Probable proteasome subunit alpha type-7
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex / Proteasome / Inhibitor / Binding Analysis
Function / homology
Function and homology information


proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / proteasomal ubiquitin-independent protein catabolic process / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis ...proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / proteasomal ubiquitin-independent protein catabolic process / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / proteasome endopeptidase complex / endopeptidase activator activity / proteasome core complex, beta-subunit complex / proteasome assembly / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / Neutrophil degranulation / proteasome complex / peroxisome / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol
Similarity search - Function
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. ...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
Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 ...Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHuber, E.M. / Groll, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationGR1861/10-1 Germany
German Research FoundationSFB1035/A2 Germany
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Systematic Analyses of Substrate Preferences of 20S Proteasomes Using Peptidic Epoxyketone Inhibitors.
Authors: Huber, E.M. / de Bruin, G. / Heinemeyer, W. / Paniagua Soriano, G. / Overkleeft, H.S. / Groll, M.
History
DepositionFeb 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_validate_close_contact.auth_atom_id_2 / _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_conn_type.id
Revision 2.1Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)734,64950
Polymers733,52134
Non-polymers1,12816
Water7,692427
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.190, 299.330, 144.940
Angle α, β, γ (deg.)90.00, 112.97, 90.00
Int Tables number4
Space group name H-MP1211
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:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 300
2111O1 - 300
1121B1 - 300
2121P1 - 300
1131C1 - 300
2131Q1 - 300
1141D1 - 300
2141R1 - 300
1151E1 - 300
2151S1 - 300
1161F1 - 300
2161T1 - 300
1171G1 - 300
2171U1 - 300
1181H1 - 300
2181V1 - 300
1191I1 - 300
2191W1 - 300
11101J1 - 300
21101X1 - 300
11111K1 - 300
21111Y1 - 300
11121L1 - 300
21121Z1 - 300
11131M1 - 300
21131a1 - 300
11141N1 - 300
21141b1 - 300

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

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999603, -0.001329, 0.028134), (-0.00348, -0.985406, -0.170188), (0.02795, -0.170218, 0.98501)68.07388, -288.483, -25.58134

-
Components

-
Proteasome subunit alpha type- ... , 6 types, 12 molecules AOBPCQDRESGU

#1: Protein Proteasome subunit alpha type-2 / Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / ...Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / Proteinase YSCE subunit 7


Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P23639, proteasome endopeptidase complex
#2: Protein Proteasome subunit alpha type-3 / Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteasome component Y13 ...Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteasome component Y13 / Proteinase YSCE subunit 13


Mass: 28748.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P23638, proteasome endopeptidase complex
#3: Protein Proteasome subunit alpha type-4 / Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteasome component ...Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteasome component PRE6 / Proteinase YSCE subunit PRE6


Mass: 28478.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P40303, proteasome endopeptidase complex
#4: Protein Proteasome subunit alpha type-5 / Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteasome component ...Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteasome component PUP2 / Proteinase YSCE subunit PUP2


Mass: 28649.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P32379, proteasome endopeptidase complex
#5: Protein Proteasome subunit alpha type-6 / Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteasome component ...Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteasome component PRE5 / Proteinase YSCE subunit PRE5


Mass: 25634.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P40302, proteasome endopeptidase complex
#7: Protein Proteasome subunit alpha type-1 / Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7- ...Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7-alpha / Proteasome component Y8 / Proteinase YSCE subunit 7 / SCL1 suppressor protein


Mass: 28033.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P21243, proteasome endopeptidase complex

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

#8: Protein Proteasome subunit beta type-2 / Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteasome component ...Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteasome component PUP1 / Proteinase YSCE subunit PUP1


Mass: 25114.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P25043, proteasome endopeptidase complex
#9: Protein Proteasome subunit beta type-3 / Macropain subunit PUP3 / Multicatalytic endopeptidase complex subunit PUP3 / Proteasome component PUP3


Mass: 22627.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P25451, proteasome endopeptidase complex
#10: Protein Proteasome subunit beta type-4 / Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteasome component C11 ...Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteasome component C11 / Proteinase YSCE subunit 11


Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P22141, proteasome endopeptidase complex
#11: Protein Proteasome subunit beta type-5 / Macropain subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2 / Proteasome component ...Macropain subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2 / Proteasome component PRE2 / Proteinase YSCE subunit PRE2


Mass: 23325.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P30656, proteasome endopeptidase complex
#12: Protein Proteasome subunit beta type-6 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5


Mass: 24883.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P23724, proteasome endopeptidase complex
#13: Protein Proteasome subunit beta type-7 / Macropain subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4 / Proteasome component ...Macropain subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4 / Proteasome component PRE4 / Proteinase YSCE subunit PRE4


Mass: 27200.893 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P30657, proteasome endopeptidase complex
#14: Protein Proteasome subunit beta type-1 / Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component ...Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component PRE3 / Proteinase YSCE subunit PRE3


Mass: 21517.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P38624, proteasome endopeptidase complex

-
Protein / Protein/peptide , 2 types, 8 molecules FTcdefgh

#15: Protein/peptide
Ac-PLL-ep


Mass: 411.622 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: Protein Probable proteasome subunit alpha type-7 / Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteasome component C1 / ...Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteasome component C1 / Proteinase YSCE subunit 1


Mass: 31575.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P21242, proteasome endopeptidase complex

-
Non-polymers , 4 types, 443 molecules

#16: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#17: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#18: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#19: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 3.67 Å3/Da / Density % sol: 66.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 20 mM MgAC2, 13% MPD, 0.1 M MES / PH range: 6.8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2014
RadiationMonochromator: LN2 COOLED FIXED-EXIT. SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 283018 / Num. obs: 283018 / % possible obs: 97 % / Redundancy: 3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.8
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.3 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMAC5.7.0032refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RYP

1ryp


Resolution: 2.7→15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.937 / SU B: 25.271 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22423 14151 5 %RANDOM
Rwork0.19795 ---
obs0.19926 268867 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.167 Å2
Baniso -1Baniso -2Baniso -3
1-4.33 Å2-0 Å2-0.74 Å2
2---6.74 Å20 Å2
3---2 Å2
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49277 0 246 427 49950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01950451
X-RAY DIFFRACTIONr_bond_other_d0.0020.0248301
X-RAY DIFFRACTIONr_angle_refined_deg0.9261.96868278
X-RAY DIFFRACTIONr_angle_other_deg0.7913.002111215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.33856308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87224.4062247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.285158737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.95515284
X-RAY DIFFRACTIONr_chiral_restr0.0530.27709
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0257137
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0211285
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_it2.455.53725316
X-RAY DIFFRACTIONr_mcbond_other2.455.53625315
X-RAY DIFFRACTIONr_mcangle_it3.2468.28931593
X-RAY DIFFRACTIONr_mcangle_other3.2468.28931594
X-RAY DIFFRACTIONr_scbond_it2.335.85225135
X-RAY DIFFRACTIONr_scbond_other2.335.85125135
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.98.65536685
X-RAY DIFFRACTIONr_long_range_B_refined3.66642.92353798
X-RAY DIFFRACTIONr_long_range_B_other3.65742.92553771
X-RAY DIFFRACTIONr_rigid_bond_restr1.047398752
X-RAY DIFFRACTIONr_sphericity_free28.515250
X-RAY DIFFRACTIONr_sphericity_bonded19.193598034
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3099TIGHT POSITIONAL00.05
1A3274TIGHT POSITIONAL00.05
1A3439TIGHT POSITIONAL00.05
1A3618TIGHT POSITIONAL00.05
1A3022TIGHT POSITIONAL00.05
1A3795TIGHT THERMAL5.580.5
2B3756TIGHT THERMAL4.840.5
3C3729TIGHT THERMAL11.50.5
4D3578TIGHT THERMAL7.50.5
5E3509TIGHT THERMAL5.420.5
6F3749TIGHT THERMAL6.440.5
7G3770TIGHT THERMAL4.910.5
8H3395TIGHT THERMAL4.220.5
9I3119TIGHT THERMAL3.890.5
10J3099TIGHT THERMAL3.720.5
11K3274TIGHT THERMAL3.760.5
12L3439TIGHT THERMAL3.770.5
13M3618TIGHT THERMAL3.680.5
14N3022TIGHT THERMAL3.470.5
LS refinement shellResolution: 2.7→2.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 1025 -
Rwork0.311 19472 -
obs--98.33 %
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)
10.0550.03810.05350.13360.03740.0569-0.00080.0152-0.01040.00090.0055-0.0201-0.00580.0004-0.00470.0904-0.0083-0.00050.0544-0.00070.089167.399-91.907445.9507
20.05940.0450.04130.03640.03040.0337-0.00120.0049-0.0101-0.01130.00730.00090.01240.0166-0.00610.101-0.00390.01240.05850.00250.087860.167-87.797116.392
30.02530.01710.00980.01570.00840.00670.01190.0014-0.0074-0.0113-0.00040.001-0.0081-0.004-0.01150.09920.0068-0.00330.05690.00440.088632.9255-87.1911.0642
40.00250.0064-0.00170.02960.0050.0122-0.0037-0.00870.0071-0.0186-0.00930.051-0.02120.0130.0130.07610.0115-0.01470.04490.01060.1073.6714-89.78113.5709
50.0002-0.0007-0.00020.00480.00070.0006-0.0048-0.0014-0.00160.00950.0030.02310.0033-0.00340.00180.04970.01540.02010.0593-0.00140.1352-2.6687-94.005545.544
60.00480.00420.00470.0140.00920.00710.01020.0015-0.00580.0368-0.01190.01740.0259-0.00260.00160.1049-0.00340.04020.0481-0.01350.058615.6984-94.597969.7063
70.03330.00220.00750.0080.00350.00530.00240.02050.01370.0292-0.0101-0.00410.0107-0.00490.00770.1456-0.00560.0030.0412-0.00820.072648.1636-93.136471.011
80.01190.02140.00950.06370.0260.01510.01190.0051-0.00120.0238-0.0039-0.0449-0.0077-0.0066-0.0080.0923-0.0024-0.01910.0514-0.0040.097467.7002-129.861648.1255
90.0707-0.0536-0.03960.05330.02520.03020.00730.006-0.0041-0.0021-0.0075-0.0305-0.0277-0.01450.00020.0845-0.00410.00990.0616-0.0010.103368.729-127.347520.9224
100.04210.03820.0160.13160.02140.00720.00180.0020.0117-0.03750.0043-0.004-0.00030.004-0.00620.11480.0012-0.00090.0556-0.00010.083945.2121-126.3946-0.5035
110.07580.05430.00190.131-0.00020.06350.00050.01150.0068-0.04240.00650.0347-0.01570.0162-0.0070.09580.0055-0.03140.05330.01160.09411.4438-130.56432.5768
120.11210.0130.05080.0414-0.04160.09420.0061-0.00820.02050.021-0.00070.0344-0.0089-0.0031-0.00540.0650.0093-0.00820.05160.00580.1206-4.0246-133.815728.6283
130.07790.02680.01560.2462-0.01710.01240.014-0.00110.02090.0594-0.01770.04580.0052-0.00380.00380.1029-0.00230.01820.0554-0.00510.0928.2072-137.386460.3787
140.0188-0.018-0.01830.24450.07380.0330.01890.00140.00740.0587-0.0077-0.0064-0.00050.0056-0.01120.1389-0.0075-0.00440.05850.00290.076840.2365-133.731970.5271
150.1098-0.0464-0.0840.02330.04090.0732-0.00460.01540.00390.01020.0038-0.00010.0233-0.00040.00080.0871-0.0121-0.01940.05540.01070.10651.9924-205.881336.9855
160.09070.02950.04980.0247-0.00990.08-0.00540.00270.0048-0.01060.00360.0011-0.012-0.00720.00170.09730.0028-0.02810.0556-0.0080.10058.4487-204.81686.9683
170.03350.01760.01360.02260.00190.01550.0097-0.0118-0.0099-0.03050.00180.01550.00790.0131-0.01150.11470.02-0.00830.0405-0.02210.073935.662-202.9785-8.8524
180.0083-0.01340.00780.0601-0.03950.0262-0.0063-0.01060.0179-0.0307-0.0111-0.03220.02240.00840.01730.05850.03150.01890.0312-0.020.071465.0955-202.46083.4973
190.00340.00370.00090.00440.00130.00070.01080.0036-0.01450.0129-0.0002-0.0210.0018-0.0028-0.01060.06480.0237-0.02680.044-0.0030.147572.0819-203.652735.4639
200.0280.0239-0.01730.0212-0.01310.01340.03090.0016-0.03630.0473-0.0259-0.0344-0.029-0.0095-0.00510.1166-0.0122-0.05440.02780.00710.104554.1633-207.17159.6859
210.0227-0.0228-0.01590.06980.00640.01550.00130.00570.00270.02080.0016-0.0002-0.00310.0045-0.00290.1148-0.0108-0.01610.0460.00630.087421.8392-209.111161.3011
220.00450.0141-0.00280.0638-0.01330.0060.012-0.00120.00170.0193-0.00840.04730.01140.0041-0.00350.0868-0.0076-0.00250.0510.00720.11021.8322-168.87745.5302
230.0456-0.0330.06040.0826-0.04070.08890.00190.0035-0.0049-0.02370.00250.04050.02740.0142-0.00440.0849-0.005-0.02060.04850.00410.11880.2882-166.726718.2541
240.02970.02350.0010.02830.00050.00110.00640.0071-0.0046-0.01930.00560.016-0.00420.0019-0.01190.11510.0059-0.02080.0617-0.00250.088723.4082-164.0046-3.518
250.05590.04270.02130.04940.0120.02290.00610.0009-0.0011-0.02430.0068-0.02210.01060.006-0.01290.08550.01180.01690.0546-0.01260.066257.2371-160.3874-0.4027
260.03810.00610.00660.2043-0.01510.01130.02310.01-0.0221-0.0021-0.0121-0.08750.0083-0.0051-0.01110.04470.0030.00840.0677-0.00340.094168.9559-160.035926.2267
270.0449-0.0842-0.02120.20120.05010.06380.00340.0057-0.00930.0529-0.0052-0.02310.0020.00690.00190.1045-0.0025-0.02710.05750.00640.089161.5441-163.435157.6101
280.0928-0.01760.04950.13020.05060.0550.0153-0.0087-0.01530.0259-0.0046-0.00120.0162-0.0085-0.01070.1267-0.00950.00050.05890.00290.074929.723-168.875167.6762
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999
5X-RAY DIFFRACTION5E-10 - 9999
6X-RAY DIFFRACTION6F-10 - 9999
7X-RAY DIFFRACTION7G-10 - 9999
8X-RAY DIFFRACTION8H-10 - 9999
9X-RAY DIFFRACTION9I-10 - 9999
10X-RAY DIFFRACTION10J-10 - 9999
11X-RAY DIFFRACTION11K-10 - 9999
12X-RAY DIFFRACTION12L-10 - 9999
13X-RAY DIFFRACTION13M-10 - 9999
14X-RAY DIFFRACTION14N-10 - 9999
15X-RAY DIFFRACTION15O-10 - 9999
16X-RAY DIFFRACTION16P-10 - 9999
17X-RAY DIFFRACTION17Q-10 - 9999
18X-RAY DIFFRACTION18R-10 - 9999
19X-RAY DIFFRACTION19S-10 - 9999
20X-RAY DIFFRACTION20T-10 - 9999
21X-RAY DIFFRACTION21U-10 - 9999
22X-RAY DIFFRACTION22V-10 - 9999
23X-RAY DIFFRACTION23W-10 - 9999
24X-RAY DIFFRACTION24X-10 - 9999
25X-RAY DIFFRACTION25Y-10 - 9999
26X-RAY DIFFRACTION26Z-10 - 9999
27X-RAY DIFFRACTION27a-10 - 9999
28X-RAY DIFFRACTION28b-10 - 9999

+
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