[English] 日本語
Yorodumi
- PDB-4qvy: yCP beta5-A49T-mutant in complex with bortezomib -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qvy
TitleyCP beta5-A49T-mutant in complex with bortezomib
Components
  • (PROTEASOME SUBUNIT ALPHA TYPE- ...) x 6
  • (PROTEASOME SUBUNIT BETA TYPE- ...) x 7
  • PROBABLE PROTEASOME SUBUNIT ALPHA TYPE-7
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Cancer / Proteasome / Bortezomib / Drug Resistance / Binding Analysis / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ub-specific processing proteases / proteasome storage granule / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex ...proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ub-specific processing proteases / proteasome storage granule / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / Neutrophil degranulation / proteasome complex / proteasomal protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol / cytoplasm
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 alpha6 / Proteasome subunit alpha5 / 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 alpha6 / Proteasome subunit alpha5 / 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 alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-BO2 / 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 ...Chem-BO2 / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsHuber, E.M. / Heinemeyer, W. / Groll, M.
CitationJournal: Structure / Year: 2015
Title: Bortezomib-Resistant Mutant Proteasomes: Structural and Biochemical Evaluation with Carfilzomib and ONX 0914.
Authors: Huber, E.M. / Heinemeyer, W. / Groll, M.
History
DepositionJul 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)733,77747
Polymers731,11128
Non-polymers2,66619
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area124520 Å2
ΔGint-489 kcal/mol
Surface area214800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.320, 300.900, 144.920
Angle α, β, γ (deg.)90.00, 112.81, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999624, -0.002475, 0.027305), (-0.002284, -0.984935, -0.172909), (0.027321, -0.172906, 0.984559)67.43683, -289.29828, -26.07954

-
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 / Mutation: A49T / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
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 (brewer's yeast) / Strain: ATCC 204508 / S288c
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 (brewer's yeast) / Strain: ATCC 204508 / S288c
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 (brewer's yeast) / Strain: ATCC 204508 / S288c
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 (brewer's yeast) / Strain: ATCC 204508 / S288c
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 (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P21243, proteasome endopeptidase complex

-
Protein , 1 types, 2 molecules FT

#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 (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P21242, proteasome endopeptidase complex

-
PROTEASOME SUBUNIT BETA TYPE- ... , 7 types, 14 molecules HVIWJXKYLZMaNb

#8: Protein PROTEASOME SUBUNIT BETA TYPE-2 / PSMB2 / 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 (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P25043, proteasome endopeptidase complex
#9: Protein PROTEASOME SUBUNIT BETA TYPE-3 / PSMB3 / 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 (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P25451, proteasome endopeptidase complex
#10: Protein PROTEASOME SUBUNIT BETA TYPE-4 / PSMB4 / 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 (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P22141, proteasome endopeptidase complex
#11: Protein PROTEASOME SUBUNIT BETA TYPE-5 / PSMB5 / 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: 23355.275 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: PRE2, DOA3, PRG1, YPR103W, P8283.10 / Production host: SACCHAROMYCES CEREVISIAE (brewer's 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 (brewer's yeast) / Strain: ATCC 204508 / S288c
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 (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P30657, proteasome endopeptidase complex
#14: Protein PROTEASOME SUBUNIT BETA TYPE-1 / PSMB1 / 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 (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P38624, proteasome endopeptidase complex

-
Non-polymers , 4 types, 445 molecules

#15: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#16: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#17: Chemical
ChemComp-BO2 / N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE / BORTEZOMIB / Bortezomib


Mass: 384.237 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C19H25BN4O4 / Comment: medication, anticancer*YM
#18: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 426 / 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, PH 6.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 13, 2012
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: 2.5→30 Å / Num. all: 366982 / Num. obs: 362946 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 16.4
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 3.9 / % possible all: 92.3

-
Processing

Software
NameClassification
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RYP

1ryp


Resolution: 2.51→15 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 19.95 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2189 18148 5 %RANDOM
Rwork0.1933 ---
all0.198 362946 --
obs0.19458 344798 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.692 Å2
Baniso -1Baniso -2Baniso -3
1-4.65 Å20 Å2-1.74 Å2
2---5.89 Å2-0 Å2
3---1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.51→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49370 0 181 426 49977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01950458
X-RAY DIFFRACTIONr_bond_other_d0.0020.0248198
X-RAY DIFFRACTIONr_angle_refined_deg0.8991.96768268
X-RAY DIFFRACTIONr_angle_other_deg0.7053.001110972
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.17356314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44724.4232252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.411158754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.34215284
X-RAY DIFFRACTIONr_chiral_restr0.050.27688
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0257252
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0211322
X-RAY DIFFRACTIONr_mcbond_it2.1755.425346
X-RAY DIFFRACTIONr_mcbond_other2.1755.39925345
X-RAY DIFFRACTIONr_mcangle_it2.8738.08331630
X-RAY DIFFRACTIONr_mcangle_other2.8738.08331631
X-RAY DIFFRACTIONr_scbond_it2.1235.82225112
X-RAY DIFFRACTIONr_scbond_other2.1235.82225112
X-RAY DIFFRACTIONr_scangle_other2.5898.57236638
X-RAY DIFFRACTIONr_long_range_B_refined3.23942.13353875
X-RAY DIFFRACTIONr_long_range_B_other3.22542.12953839
X-RAY DIFFRACTIONr_rigid_bond_restr1.84398656
X-RAY DIFFRACTIONr_sphericity_free27.5365269
X-RAY DIFFRACTIONr_sphericity_bonded16.48597917
LS refinement shellResolution: 2.505→2.568 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 1263 -
Rwork0.309 24001 -
obs--96.74 %
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)
10.068-0.02250.04750.011-0.01610.0403-0.00210.0131-0.00470.00070.0005-0.0115-0.0197-0.00130.00160.084-0.01260.00660.0674-0.00310.114967.2563-92.136846.0876
20.0009-0.0022-0.00570.01250.03060.10020.0031-0.0011-0.0065-0.0103-0.0069-0.0007-0.00790.01690.00380.0862-0.01050.02020.06830.0060.107259.8251-87.928216.4332
30.03770.02090.00030.0205-0.01570.03950.0104-0.00170.0054-0.00410.00430.0173-0.00540.0213-0.01470.10910.00480.00160.06120.00380.100732.5228-87.36911.1374
40.0466-0.03220.04540.0283-0.02740.0477-0.0048-0.0039-0.0064-0.0074-0.00120.0262-0.0168-0.00590.0060.06040.0295-0.00230.03840.00820.11683.2296-90.059913.7055
50.0807-0.0120.04910.0059-0.00620.0309-0.0061-0.022-0.0160.0080.00580.0224-0.0044-0.00950.00020.01940.01680.02770.0699-0.0060.1093-3.0502-94.320145.8725
60.0219-0.0048-0.01930.0139-0.00980.04170.0031-0.0030.00260.02180.00880.0067-0.0018-0.0014-0.01190.10990.00260.02630.068-0.00650.101615.4731-94.988370.0418
70.00890.00610.0140.01380.02610.05760.01010.01280.00240.0194-0.0103-0.00130.01-0.01020.00030.1381-0.0079-0.00060.0543-0.00910.101247.9851-93.437171.2856
80.00550.0137-0.00130.0583-0.00220.00240.0151-0.0060.00080.0482-0.0079-0.0486-0.007-0.0082-0.00720.05690.0008-0.00670.057-0.00230.11367.8393-129.659647.6021
90.0084-0.0370.02090.38480.11780.329-0.00180.01240.0070.0008-0.0082-0.0217-0.03430.01320.010.0179-0.0070.03530.07950.00650.10668.4977-127.570520.9387
100.08830.07580.03240.07670.02610.01450.0055-0.00190.0024-0.0280.0054-0.00620.01090.0035-0.01090.10710.00230.01560.07080.00180.095244.8584-126.6114-0.6522
110.00320.00080.01270.11930.01240.09860.00790.0059-0.0007-0.03980.01030.0287-0.0156-0.0018-0.01820.0560.0067-0.00390.050.01230.091111.001-130.89022.5721
120.0425-0.00430.05750.08490.02980.13080.0021-0.02090.003-0.00450.00760.0369-0.01810.0104-0.00980.0130.00120.01810.07880.00720.1281-4.4534-134.357328.6943
130.0097-0.02590.00760.28680.00130.01090.0055-0.00510.0060.0396-0.010.017-0.0039-0.00810.00450.06060.00010.03230.0736-0.0010.10117.97-137.881660.5858
140.0681-0.0368-0.02490.09220.00390.01280.0136-0.0074-0.00390.0386-0.00380.0175-0.0029-0.0043-0.00980.1151-0.0068-0.00410.0648-0.0010.087740.04-134.17170.8928
150.05980.00710.00550.04130.04030.05110.00580.0090.007-0.0038-0.00190.00430.0259-0.0001-0.00380.0865-0.0173-0.01160.05870.01180.11761.7025-206.667236.955
160.00530.00240.00250.00160.00180.0023-0.01080.0044-0.0026-0.00670.00170.0065-0.00460.00340.00910.1041-0.003-0.02080.058-0.00350.11428.341-205.64566.8195
170.0095-0.00260.00910.0059-0.0070.0280.0124-0.0108-0.0032-0.02320.00280.00820.0120.013-0.01520.10910.0308-0.00340.0463-0.01420.099935.4935-203.7019-9.0068
180.0162-0.0320.00590.0784-0.0220.00940.0134-0.00310.0291-0.0574-0.0206-0.05250.02330.01460.00720.05810.0340.03030.0376-0.01770.101165.0289-203.12743.381
190.03020.009-0.00480.00770.00140.00770.0187-0.0012-0.0030.0093-0.0076-0.02560.0045-0.0079-0.01110.04750.0199-0.00920.0596-0.00560.130972.003-204.308335.5471
200.0488-0.00010.03930.0018-0.00130.03470.0248-0.0062-0.00960.0061-0.0171-0.00720.0147-0.0076-0.00780.10330.0037-0.02710.04340.00960.108254.0033-207.819859.8172
210.01540.0011-0.00590.0157-0.01530.0194-0.0026-0.0023-0.00410.00090.00120.0176-0.00430.00890.00140.1237-0.0076-0.00880.05960.00910.110721.5814-209.843661.4265
220.00850.01240.00550.02960.00090.01310.0158-0.01190.00250.0231-0.00340.03280.0217-0.0103-0.01240.0546-0.00850.01130.06290.00910.11011.2301-169.948444.9002
230.0021-0.01310.00350.2144-0.03030.00840.00610.008-0.005-0.0063-0.0040.02940.01760.0056-0.00210.0809-0.0002-0.01780.06690.00170.12170.0123-167.454618.2092
240.02840.0636-0.00770.1646-0.01810.0046-0.0010.0003-0.0053-0.04580.01030.0191-0.00380.0059-0.00930.10840.0044-0.01530.0663-0.00080.103223.186-164.6773-3.7692
250.0493-0.03110.07020.1344-0.0370.10590.01810.0126-0.0161-0.069-0.0067-0.02310.02580.0053-0.01140.04660.01210.03670.053-0.010.092757.0921-161.1172-0.5534
260.02720.0029-0.03720.1801-0.03980.09090.0113-0.0082-0.01190.0311-0.0165-0.05940.0047-0.00150.00520.04410.0080.00440.0754-0.00020.132673.0923-161.989325.4603
270.0167-0.0202-0.00420.1480.03440.010.00870.0133-0.01250.0555-0.0085-0.03720.0081-0.0039-0.00020.0869-0.0015-0.01020.06520.00520.107861.3764-163.962857.7316
280.0397-0.03690.02710.0549-0.02910.02080.01960.0003-0.00470.0242-0.0078-0.0090.0012-0.002-0.01180.1137-0.00530.00150.062800.094929.5464-169.45467.9825
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 250
2X-RAY DIFFRACTION1A301 - 312
3X-RAY DIFFRACTION2B1 - 244
4X-RAY DIFFRACTION2B301 - 314
5X-RAY DIFFRACTION3C1 - 240
6X-RAY DIFFRACTION3C301 - 312
7X-RAY DIFFRACTION4D1 - 242
8X-RAY DIFFRACTION4D301 - 307
9X-RAY DIFFRACTION5E3 - 233
10X-RAY DIFFRACTION5E301 - 306
11X-RAY DIFFRACTION6F2 - 244
12X-RAY DIFFRACTION6F301 - 315
13X-RAY DIFFRACTION7G2 - 242
14X-RAY DIFFRACTION7G301 - 302
15X-RAY DIFFRACTION7G401 - 418
16X-RAY DIFFRACTION8H1 - 226
17X-RAY DIFFRACTION8H301
18X-RAY DIFFRACTION8H401 - 431
19X-RAY DIFFRACTION9I1 - 204
20X-RAY DIFFRACTION9I301
21X-RAY DIFFRACTION9I401 - 413
22X-RAY DIFFRACTION10J1 - 195
23X-RAY DIFFRACTION10J201
24X-RAY DIFFRACTION10J301 - 313
25X-RAY DIFFRACTION11K1 - 212
26X-RAY DIFFRACTION11K301 - 303
27X-RAY DIFFRACTION11K401 - 419
28X-RAY DIFFRACTION12L1 - 222
29X-RAY DIFFRACTION12L301 - 324
30X-RAY DIFFRACTION13M1 - 233
31X-RAY DIFFRACTION13M301 - 324
32X-RAY DIFFRACTION14N1 - 196
33X-RAY DIFFRACTION14N201 - 203
34X-RAY DIFFRACTION14N301 - 313
35X-RAY DIFFRACTION15O1 - 250
36X-RAY DIFFRACTION15O301 - 315
37X-RAY DIFFRACTION16P1 - 244
38X-RAY DIFFRACTION16P301 - 312
39X-RAY DIFFRACTION17Q1 - 240
40X-RAY DIFFRACTION17Q301 - 306
41X-RAY DIFFRACTION18R1 - 242
42X-RAY DIFFRACTION18R301 - 307
43X-RAY DIFFRACTION19S3 - 233
44X-RAY DIFFRACTION19S301 - 305
45X-RAY DIFFRACTION20T2 - 244
46X-RAY DIFFRACTION20T301 - 313
47X-RAY DIFFRACTION21U2 - 242
48X-RAY DIFFRACTION21U301
49X-RAY DIFFRACTION21U401 - 415
50X-RAY DIFFRACTION22V1 - 226
51X-RAY DIFFRACTION22V301 - 302
52X-RAY DIFFRACTION22V401 - 423
53X-RAY DIFFRACTION23W1 - 204
54X-RAY DIFFRACTION23W301 - 307
55X-RAY DIFFRACTION24X1 - 195
56X-RAY DIFFRACTION24X201 - 219
57X-RAY DIFFRACTION25Y1 - 212
58X-RAY DIFFRACTION25Y301 - 302
59X-RAY DIFFRACTION25Y401 - 418
60X-RAY DIFFRACTION26Z1 - 222
61X-RAY DIFFRACTION26Z301
62X-RAY DIFFRACTION26Z401 - 415
63X-RAY DIFFRACTION27a1 - 233
64X-RAY DIFFRACTION27a301 - 330
65X-RAY DIFFRACTION28b1 - 196
66X-RAY DIFFRACTION28b201 - 202
67X-RAY DIFFRACTION28b301 - 320

+
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