[English] 日本語
Yorodumi
- PDB-5lhy: PB3 Domain of Human PLK4 (apo) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lhy
TitlePB3 Domain of Human PLK4 (apo)
ComponentsSerine/threonine-protein kinase PLK4
KeywordsSTRUCTURAL PROTEIN / Polo box domain / Centriole / transferase
Function / homology
Function and homology information


de novo centriole assembly involved in multi-ciliated epithelial cell differentiation / procentriole / deuterosome / procentriole replication complex / positive regulation of centriole replication / trophoblast giant cell differentiation / polo kinase / XY body / cleavage furrow / centriole replication ...de novo centriole assembly involved in multi-ciliated epithelial cell differentiation / procentriole / deuterosome / procentriole replication complex / positive regulation of centriole replication / trophoblast giant cell differentiation / polo kinase / XY body / cleavage furrow / centriole replication / cilium assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / centriole / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / nucleolus / ATP binding / identical protein binding / cytosol
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #930 / Serine/threonine-protein kinase, first cryptic polo-box domain superfamily / : / Cryptic Polo-Box 1 (CPB1) domain profile. / Cryptic Polo-Box 2 (CPB2) domain profile. / Plk4, C-terminal polo-box domain / Plk4, second cryptic polo-box domain / Plk4, first cryptic polo-box domain / Polo-like Kinase 4 Polo Box 1 / Polo-like Kinase 4 Polo Box 2 ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #930 / Serine/threonine-protein kinase, first cryptic polo-box domain superfamily / : / Cryptic Polo-Box 1 (CPB1) domain profile. / Cryptic Polo-Box 2 (CPB2) domain profile. / Plk4, C-terminal polo-box domain / Plk4, second cryptic polo-box domain / Plk4, first cryptic polo-box domain / Polo-like Kinase 4 Polo Box 1 / Polo-like Kinase 4 Polo Box 2 / POLO box domain / POLO box domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Tyrosine-protein kinase, active site / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase PLK4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 Å
AuthorsCottee, M.A. / Johnson, S. / Lea, S.M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust100298 United Kingdom
Wellcome Trust104575 United Kingdom
CitationJournal: Biol Open / Year: 2017
Title: A key centriole assembly interaction interface between human PLK4 and STIL appears to not be conserved in flies.
Authors: Cottee, M.A. / Johnson, S. / Raff, J.W. / Lea, S.M.
History
DepositionJul 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Mar 29, 2017Group: Database references
Revision 1.3May 10, 2017Group: Database references
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK4
B: Serine/threonine-protein kinase PLK4
C: Serine/threonine-protein kinase PLK4
D: Serine/threonine-protein kinase PLK4
E: Serine/threonine-protein kinase PLK4
F: Serine/threonine-protein kinase PLK4
G: Serine/threonine-protein kinase PLK4
H: Serine/threonine-protein kinase PLK4
I: Serine/threonine-protein kinase PLK4
J: Serine/threonine-protein kinase PLK4
K: Serine/threonine-protein kinase PLK4
L: Serine/threonine-protein kinase PLK4
M: Serine/threonine-protein kinase PLK4
N: Serine/threonine-protein kinase PLK4
O: Serine/threonine-protein kinase PLK4
P: Serine/threonine-protein kinase PLK4
Q: Serine/threonine-protein kinase PLK4
R: Serine/threonine-protein kinase PLK4
S: Serine/threonine-protein kinase PLK4
T: Serine/threonine-protein kinase PLK4
U: Serine/threonine-protein kinase PLK4
V: Serine/threonine-protein kinase PLK4
W: Serine/threonine-protein kinase PLK4
X: Serine/threonine-protein kinase PLK4
Y: Serine/threonine-protein kinase PLK4
Z: Serine/threonine-protein kinase PLK4
1: Serine/threonine-protein kinase PLK4
2: Serine/threonine-protein kinase PLK4
3: Serine/threonine-protein kinase PLK4
4: Serine/threonine-protein kinase PLK4
5: Serine/threonine-protein kinase PLK4
6: Serine/threonine-protein kinase PLK4
7: Serine/threonine-protein kinase PLK4
8: Serine/threonine-protein kinase PLK4
9: Serine/threonine-protein kinase PLK4
a: Serine/threonine-protein kinase PLK4
b: Serine/threonine-protein kinase PLK4
c: Serine/threonine-protein kinase PLK4
d: Serine/threonine-protein kinase PLK4
e: Serine/threonine-protein kinase PLK4
f: Serine/threonine-protein kinase PLK4
g: Serine/threonine-protein kinase PLK4
h: Serine/threonine-protein kinase PLK4
i: Serine/threonine-protein kinase PLK4
j: Serine/threonine-protein kinase PLK4
k: Serine/threonine-protein kinase PLK4
l: Serine/threonine-protein kinase PLK4
m: Serine/threonine-protein kinase PLK4
n: Serine/threonine-protein kinase PLK4
o: Serine/threonine-protein kinase PLK4
p: Serine/threonine-protein kinase PLK4
q: Serine/threonine-protein kinase PLK4
r: Serine/threonine-protein kinase PLK4
s: Serine/threonine-protein kinase PLK4
t: Serine/threonine-protein kinase PLK4
u: Serine/threonine-protein kinase PLK4
v: Serine/threonine-protein kinase PLK4
w: Serine/threonine-protein kinase PLK4
x: Serine/threonine-protein kinase PLK4
y: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)594,91160
Polymers594,91160
Non-polymers00
Water0
1
A: Serine/threonine-protein kinase PLK4
B: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-23 kcal/mol
Surface area9590 Å2
MethodPISA
2
C: Serine/threonine-protein kinase PLK4
D: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-24 kcal/mol
Surface area9570 Å2
MethodPISA
3
E: Serine/threonine-protein kinase PLK4
F: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-22 kcal/mol
Surface area9550 Å2
MethodPISA
4
G: Serine/threonine-protein kinase PLK4
H: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-23 kcal/mol
Surface area9550 Å2
MethodPISA
5
I: Serine/threonine-protein kinase PLK4
J: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-23 kcal/mol
Surface area9590 Å2
MethodPISA
6
K: Serine/threonine-protein kinase PLK4
L: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-23 kcal/mol
Surface area9670 Å2
MethodPISA
7
M: Serine/threonine-protein kinase PLK4
N: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-22 kcal/mol
Surface area9630 Å2
MethodPISA
8
O: Serine/threonine-protein kinase PLK4
P: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-23 kcal/mol
Surface area9540 Å2
MethodPISA
9
Q: Serine/threonine-protein kinase PLK4
R: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-23 kcal/mol
Surface area9630 Å2
MethodPISA
10
S: Serine/threonine-protein kinase PLK4
T: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-23 kcal/mol
Surface area9570 Å2
MethodPISA
11
U: Serine/threonine-protein kinase PLK4
V: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-23 kcal/mol
Surface area9530 Å2
MethodPISA
12
W: Serine/threonine-protein kinase PLK4
X: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-23 kcal/mol
Surface area9600 Å2
MethodPISA
13
Y: Serine/threonine-protein kinase PLK4
Z: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-23 kcal/mol
Surface area9610 Å2
MethodPISA
14
1: Serine/threonine-protein kinase PLK4
2: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-22 kcal/mol
Surface area9480 Å2
MethodPISA
15
3: Serine/threonine-protein kinase PLK4
4: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-23 kcal/mol
Surface area9660 Å2
MethodPISA
16
5: Serine/threonine-protein kinase PLK4
6: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-23 kcal/mol
Surface area9590 Å2
MethodPISA
17
7: Serine/threonine-protein kinase PLK4
8: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-23 kcal/mol
Surface area9600 Å2
MethodPISA
18
9: Serine/threonine-protein kinase PLK4
a: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-22 kcal/mol
Surface area9550 Å2
MethodPISA
19
b: Serine/threonine-protein kinase PLK4
c: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-22 kcal/mol
Surface area9630 Å2
MethodPISA
20
d: Serine/threonine-protein kinase PLK4
e: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-23 kcal/mol
Surface area9670 Å2
MethodPISA
21
f: Serine/threonine-protein kinase PLK4
g: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-22 kcal/mol
Surface area9620 Å2
MethodPISA
22
h: Serine/threonine-protein kinase PLK4
i: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-23 kcal/mol
Surface area9590 Å2
MethodPISA
23
j: Serine/threonine-protein kinase PLK4
k: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-23 kcal/mol
Surface area9560 Å2
MethodPISA
24
l: Serine/threonine-protein kinase PLK4
m: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-23 kcal/mol
Surface area9650 Å2
MethodPISA
25
n: Serine/threonine-protein kinase PLK4
o: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-23 kcal/mol
Surface area9560 Å2
MethodPISA
26
p: Serine/threonine-protein kinase PLK4
q: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-23 kcal/mol
Surface area9640 Å2
MethodPISA
27
r: Serine/threonine-protein kinase PLK4
s: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-22 kcal/mol
Surface area9530 Å2
MethodPISA
28
t: Serine/threonine-protein kinase PLK4
u: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-23 kcal/mol
Surface area9620 Å2
MethodPISA
29
v: Serine/threonine-protein kinase PLK4
w: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-23 kcal/mol
Surface area9540 Å2
MethodPISA
30
x: Serine/threonine-protein kinase PLK4
y: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)19,8302
Polymers19,8302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-22 kcal/mol
Surface area9650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)220.350, 220.350, 325.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein ...
Serine/threonine-protein kinase PLK4 / Polo-like kinase 4 / PLK-4 / Serine/threonine-protein kinase 18 / Serine/threonine-protein kinase Sak


Mass: 9915.191 Da / Num. of mol.: 60 / Fragment: UNP residues 884-970
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK4, SAK, STK18 / Production host: Escherichia coli B (bacteria) / Strain (production host): B834 / References: UniProt: O00444, polo kinase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.99 % / Description: cubes
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 100 nl protein solution (52.3 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 100 nl mother liquor (32.27% v/v PPG400, 100 mM NaCl, 50 mM MgCl2, unbuffered)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.31→110.18 Å / Num. obs: 119458 / % possible obs: 100 % / Redundancy: 9.7 % / CC1/2: 0.999 / Net I/σ(I): 16.6
Reflection shellHighest resolution: 3.31 Å / Rmerge(I) obs: 1.353

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Chainsaw model based on 1MBY
Resolution: 3.31→104.367 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.41
RfactorNum. reflection% reflection
Rfree0.2952 5936 4.98 %
Rwork0.2692 --
obs0.2705 119305 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.31→104.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35580 0 0 0 35580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00236300
X-RAY DIFFRACTIONf_angle_d0.52849380
X-RAY DIFFRACTIONf_dihedral_angle_d15.86521360
X-RAY DIFFRACTIONf_chiral_restr0.0445700
X-RAY DIFFRACTIONf_plane_restr0.0056240
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.7226-0.43741.19137.354-0.06255.80340.1213-0.25730.78020.52030.22041.12970.0028-0.5307-0.49760.76760.0951-0.13090.69840.01241.453-50.7535-73.011315.3301
25.9580.4499-0.44034.4033-0.15026.12050.36470.2798-0.257-0.0210.16140.5578-0.1623-0.3892-0.48760.77280.034-0.18190.75660.07451.3501-51.7381-75.25798.9668
36.831-0.70620.79364.7153-1.80965.27690.37080.2595-1.22330.54870.1498-0.46471.09570.8501-0.44830.89280.0923-0.26840.8968-0.05031.4603-34.1618-89.079816.2839
46.5557-0.18353.1734.4505-0.74585.08930.30061.1285-0.4156-0.05330.2771-0.89460.58761.2491-0.68180.8350.1021-0.22660.959-0.08131.5726-31.3121-85.789411.2293
54.63510.5995-0.01295.51911.47353.9217-0.10640.087-0.0938-0.26040.2802-0.37190.13450.1804-0.20760.7670.19540.04460.93730.02080.5377-93.357-122.600141.2951
62.52620.13830.36976.94363.69464.14560.05620.44510.02030.3442-0.11040.45510.2908-0.14740.07930.74530.09860.06261.04160.12160.6625-100.0029-121.938539.1786
74.2836-0.85580.71644.81270.90046.2373-0.3215-0.69280.16151.01590.60840.1954-0.11660.1827-0.34211.13410.42180.2821.23260.23330.6254-102.3447-121.291462.6839
86.64190.5621-0.74646.9919-0.88034.8714-0.1802-1.0294-0.10361.03530.52150.90820.5756-0.0212-0.23011.31020.30270.31210.93860.17610.7392-105.5654-127.060361.1771
95.5518-1.25210.72933.4257-1.29255.33020.0588-0.24810.63980.3002-0.10840.2106-1.42270.13950.23471.40630.24390.04080.9444-0.13271.1828-1.8581-103.836938.1743
106.3988-0.08530.25596.1961.18866.6271-0.6892-0.88680.95210.41160.19030.338-0.9647-1.08640.54851.22270.22180.03790.8775-0.10061.165-7.2425-106.153241.5562
116.6901-1.84081.00093.8096-0.24774.1215-0.0674-0.2997-0.0771-0.0021-0.05810.03420.0850.430.12181.16840.11690.0460.83430.00750.99146.4278-125.343141.6436
124.7294-0.5114-0.71423.22530.69127.7809-0.32890.2675-0.53110.1950.4860.42260.8871-0.8202-0.01521.05720.2077-0.02771.00580.091.08861.0476-127.407438.1904
132.95882.4218-1.27677.4544-1.93653.9353-0.085-0.3690.13070.27220.077-0.10090.26290.32880.0420.8133-0.1039-0.06850.9656-0.04510.682-0.3273-14.036741.1586
144.21061.5131-1.01785.2171-0.34584.4149-0.03330.19940.2876-0.27060.30460.98990.3876-0.27870.21841.0306-0.227-0.0440.99750.11590.6903-6.5596-14.354638.289
154.4362.3248-1.67477.33470.5283.7237-0.6991.1741-0.362-1.51790.896-0.90080.80980.0452-0.43811.5884-0.27030.11591.1551-0.07450.68758.238-18.29419.888
166.55140.88561.17456.57420.82783.4143-0.8311.18331.006-2.37730.7692-0.28880.60.0069-0.96251.6344-0.610.0741.36750.0720.62085.283-12.457918.3955
177.77032.3832-1.61057.72880.94054.9824-0.209-1.0220.28510.891-0.16130.34220.15330.65530.43591.00870.0128-0.03790.92-0.05071.1355-64.105-97.559916.5258
185.6098-0.7986-0.01846.25081.26943.6666-0.3351-0.04110.13130.3570.19831.1516-0.2646-0.4450.17320.94780.0607-0.10690.9519-0.0530.9868-68.0192-97.405111.0092
195.9356-0.6196-1.83435.36991.27112.9779-0.43640.3087-0.67830.19160.4438-0.57160.68520.62250.09940.9831-0.08430.00731.067-0.07851.0022-49.1261-110.00624.0031
208.2625-1.2277-1.6466.02872.64915.6286-0.38511.11050.0159-0.42960.4651-0.63060.12160.9268-0.21530.8124-0.20990.05421.1851-0.12821.1674-48.7303-104.5571-0.0091
214.5454-0.0809-0.6484.16480.16577.0552-0.0110.4639-0.0627-0.40590.0507-0.6038-0.48410.4578-0.06050.9702-0.0535-0.06620.7767-0.08581.1754-65.6957-162.161259.9325
224.46260.22561.88355.44311.74827.4958-0.1693-0.07950.0740.22820.2155-0.6644-0.40880.3413-0.08660.7966-0.0389-0.19560.78840.07431.1726-66.7149-166.681665.009
235.24550.2031.48934.48851.87664.4397-0.20980.7487-0.2612-0.96490.04710.2075-0.07350.0350.17571.0113-0.0611-0.06260.7362-0.00080.9806-78.7539-176.270347.0976
245.94290.62231.94715.75981.52532.7107-0.1260.0956-0.1028-0.6210.06050.7156-0.1749-0.40940.13030.94550.002-0.04970.7543-0.08251.0443-83.5972-175.080551.5107
252.57710.48360.56044.3165-1.89468.6429-0.27860.41380.2668-0.4375-0.0017-0.21030.08850.93530.17850.7679-0.05130.04881.0753-0.0620.7179-70.3264-119.4783-9.3175
263.34982.4833-1.20725.45210.78736.6832-0.3650.7062-0.8057-0.49880.2869-0.65830.68640.86470.09380.91420.0057-0.00770.9462-0.03190.6367-68.7204-126.1382-8.3039
276.3808-0.647-1.4048.4593-0.57036.0478-0.341-0.69870.01770.50260.38180.72790.2389-0.1767-0.02060.70160.0039-0.03010.95320.07370.5458-81.5493-121.541210.855
285.9091.2247-0.37186.9465-2.60864.9130.096-1.054-0.53390.347-0.3866-0.64190.24960.55630.20080.76290.0059-0.04140.97530.05790.7171-75.3797-122.725713.599
295.3893-0.1744-2.69793.0639-0.87335.63320.20460.706-1.1336-0.681-0.40230.41260.3995-0.3060.24811.01970.0815-0.15150.8914-0.21150.9914-94.2978-138.0556-16.8578
305.92332.53190.25745.3688-1.27825.02170.23470.12980.9268-0.6511-0.24180.6061-0.09090.25650.11880.96050.07460.05630.9257-0.08830.7629-95.103-132.2015-13.5812
313.18981.2320.38054.01010.73166.8503-0.0257-0.1991-0.52520.21930.0435-0.46721.09940.55590.080.9542-0.06090.04860.8095-0.02690.7383-89.7103-147.33653.8301
324.0364-0.1486-2.03572.48-0.89637.4940.0595-0.0997-0.41010.2608-0.0940.26821.2655-0.1365-0.02360.8722-0.036-0.0610.7288-0.04720.9811-95.9927-145.53685.6362
334.5809-0.4392-0.72066.09161.13075.8335-0.3406-0.12260.9001-0.331-0.45160.9811-0.4106-1.4060.80551.19830.4299-0.05631.1630.10041.1754-9.8173-111.20613.7318
343.6566-2.4314-1.15045.1453-1.46745.6780.71310.84550.5775-0.778-0.78840.6655-1.6415-0.95010.08251.39590.55270.06251.41470.13491.3553-6.5249-106.036411.0408
353.62850.22140.85695.224-1.01336.2214-0.17610.5936-0.2465-0.16970.289-0.13050.02670.28080.02521.03360.28170.09461.14490.0141.109510.1465-122.616211.3121
363.5044-0.7993-0.96366.0876-1.48996.9870.2239-0.0431-0.4506-0.0224-0.2524-0.5531-0.57780.6075-0.00841.07250.23940.03820.9492-0.02431.198312.7062-117.834615.5648
374.57661.44850.933410.0094-1.34765.02530.030.72530.0538-1.08150.59771.2742-0.0865-0.1382-0.71281.0828-0.0138-0.22350.86580.00631.2685-32.1992-55.02698.6917
384.82760.82371.95564.9878-0.09026.7938-0.6576-0.0275-0.41140.25490.48051.4155-0.5599-0.2460.1381.2216-0.0984-0.09840.84140.09991.7384-34.1695-50.916313.522
396.38142.92731.72788.589-3.50675.70730.3047-0.4902-0.97292.10410.2246-3.01540.33510.8658-0.06931.4214-0.1148-0.72480.90690.04941.8917-18.2997-64.657424.5685
404.46840.60711.69773.8523-2.56265.0050.4814-0.7703-0.70761.4965-0.0884-0.37390.5095-0.4009-0.44931.59290.003-0.24831.01790.01221.2637-24.1779-65.900328.1336
415.9043-2.21861.73525.1787-1.52354.1034-0.9565-1.894-0.15261.31010.87140.0024-0.5811-0.83260.10751.45130.341-0.20261.41240.01330.9655-87.0068-147.622265.7365
425.0127-2.30122.368.7107-2.51556.9217-1.4576-1.95690.4812.15290.9305-1.239-1.8941-1.11160.25661.6480.421-0.35481.2083-0.13831.0056-83.7804-141.902663.7063
433.9607-4.61111.73715.3441-2.12618.32390.1266-0.6346-0.5535-0.5760.3910.86350.5756-1.6826-0.38920.9211-0.05240.0381.00490.12990.8427-93.9615-149.755543.7457
448.308-4.02071.53664.5257-2.76538.69690.61390.33-0.1629-0.5286-0.16050.55610.9595-0.2472-0.29571.03630.0183-0.03820.73320.1010.8545-87.4944-150.012642.2667
459.22082.22880.05094.979-0.95794.60320.4617-0.8224-1.50180.9633-0.4676-0.2571.13340.414-0.40941.6409-0.4563-0.24711.481-0.04742.0013-115.6324-163.8026-4.0881
465.90571.44621.98917.2516-1.65862.33851.37080.1541-1.82640.9797-0.9358-0.95741.27740.2911-1.19661.8574-0.2414-0.41731.40680.01711.9175-109.884-164.2482-7.5994
476.21673.95373.54993.43440.53054.6298-0.83010.74292.6235-0.22180.71490.34-0.5028-0.22530.20941.3616-0.2414-0.13471.4596-0.11992.2534-119.7746-143.9352-14.8784
483.17970.70431.91987.06151.09544.2459-0.42570.62441.1246-1.13410.13540.9326-0.3737-0.3902-0.47861.5819-0.2528-0.32421.46580.08081.9949-119.757-147.3393-20.842
492.9703-1.1964-0.90090.9967-1.62067.57630.33681.7329-0.1424-0.1794-0.57841.6957-0.0117-4.36180.2011.7107-0.1243-0.05243.8658-0.46111.6964-7.0498-115.6936-13.2833
504.49441.3661-4.84715.8374-2.7129.3316-0.4171.6012-0.7845-0.17510.12181.8817-0.3762-4.6480.21891.7780.2345-0.22113.6632-0.2791.698-6.6469-109.5067-16.6645
517.2681.9569-0.89194.31393.62216.185-1.1823-0.0425-0.76960.88680.2804-1.3084-0.44010.49040.64641.570.40760.18821.82830.22681.551916.4808-114.9313-14.5949
525.4403-0.11560.07662.09961.46526.50280.026-0.78230.76330.6595-0.7786-0.2915-0.5891.22110.57331.4884-0.0478-0.01181.84960.22471.785815.8923-109.0714-11.0907
534.70661.14561.09626.2102-0.21542.8322-0.46311.3029-0.7144-0.97810.2104-0.01720.71440.00780.17231.3023-0.0922-0.051.1321-0.13690.6567-11.2226-37.110911.9902
543.20341.77860.2064.5153-0.32635.9692-0.31591.27510.5089-0.72950.35520.2387-0.45450.40670.10391.396-0.2679-0.04461.170.05390.67-14.1164-31.313214.2464
555.51172.09950.77274.03330.07935.78990.1906-0.3017-0.57420.62960.1082-1.0420.52740.8928-0.20291.4164-0.2025-0.0550.9615-0.00740.8493-6.8348-41.141834.3383
564.94551.89290.59414.34782.75979.2430.769-0.4788-0.3620.4279-0.2418-0.42191.17520.3374-0.46951.3806-0.2198-0.12950.95780.07830.8038-13.5768-41.068235.1468
576.849-0.07232.76573.5136-0.1583.738-0.1454-0.0187-0.12120.4860.36150.18720.3806-0.4351-0.06691.0643-0.0399-0.15220.8202-0.07911.1141-69.8962-196.369463.8888
584.08710.07672.14773.74741.53937.93220.4650.6427-1.25660.29650.093-0.1731.35420.7754-0.59961.1745-0.0196-0.09630.914-0.07911.3311-67.7157-200.715559.0168
594.86390.96740.46693.87831.35773.7138-0.20770.2135-0.2707-0.29740.9553-1.0332-0.02341.3167-0.65970.96850.1029-0.1331.2852-0.08291.7128-48.4936-187.54262.5198
602.0321.3822-1.55754.21190.6233.8856-0.07670.43290.7987-0.48520.6961-0.6293-0.11960.9437-0.56440.8904-0.0585-0.18771.3934-0.03331.3416-50.1694-186.129856.0097
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 890 through 966)
2X-RAY DIFFRACTION2(chain 'B' and resid 890 through 966)
3X-RAY DIFFRACTION3(chain 'C' and resid 890 through 966)
4X-RAY DIFFRACTION4(chain 'D' and resid 890 through 966)
5X-RAY DIFFRACTION5(chain 'E' and resid 890 through 966)
6X-RAY DIFFRACTION6(chain 'F' and resid 890 through 966)
7X-RAY DIFFRACTION7(chain 'G' and resid 890 through 966)
8X-RAY DIFFRACTION8(chain 'H' and resid 890 through 966)
9X-RAY DIFFRACTION9(chain 'I' and resid 890 through 966)
10X-RAY DIFFRACTION10(chain 'J' and resid 890 through 966)
11X-RAY DIFFRACTION11(chain 'K' and resid 890 through 966)
12X-RAY DIFFRACTION12(chain 'L' and resid 890 through 966)
13X-RAY DIFFRACTION13(chain 'M' and resid 890 through 966)
14X-RAY DIFFRACTION14(chain 'N' and resid 890 through 966)
15X-RAY DIFFRACTION15(chain 'O' and resid 890 through 966)
16X-RAY DIFFRACTION16(chain 'P' and resid 890 through 966)
17X-RAY DIFFRACTION17(chain 'Q' and resid 890 through 966)
18X-RAY DIFFRACTION18(chain 'R' and resid 890 through 966)
19X-RAY DIFFRACTION19(chain 'S' and resid 890 through 966)
20X-RAY DIFFRACTION20(chain 'T' and resid 890 through 966)
21X-RAY DIFFRACTION21(chain 'U' and resid 890 through 966)
22X-RAY DIFFRACTION22(chain 'V' and resid 890 through 966)
23X-RAY DIFFRACTION23(chain 'W' and resid 890 through 966)
24X-RAY DIFFRACTION24(chain 'X' and resid 890 through 966)
25X-RAY DIFFRACTION25(chain 'Y' and resid 890 through 966)
26X-RAY DIFFRACTION26(chain 'Z' and resid 890 through 966)
27X-RAY DIFFRACTION27(chain '1' and resid 890 through 966)
28X-RAY DIFFRACTION28(chain '2' and resid 890 through 966)
29X-RAY DIFFRACTION29(chain '3' and resid 890 through 966)
30X-RAY DIFFRACTION30(chain '4' and resid 890 through 966)
31X-RAY DIFFRACTION31(chain '5' and resid 890 through 966)
32X-RAY DIFFRACTION32(chain '6' and resid 890 through 966)
33X-RAY DIFFRACTION33(chain '7' and resid 890 through 966)
34X-RAY DIFFRACTION34(chain '8' and resid 890 through 966)
35X-RAY DIFFRACTION35(chain '9' and resid 890 through 966)
36X-RAY DIFFRACTION36(chain 'a' and resid 890 through 966)
37X-RAY DIFFRACTION37(chain 'b' and resid 890 through 966)
38X-RAY DIFFRACTION38(chain 'c' and resid 890 through 966)
39X-RAY DIFFRACTION39(chain 'd' and resid 890 through 966)
40X-RAY DIFFRACTION40(chain 'e' and resid 890 through 966)
41X-RAY DIFFRACTION41(chain 'f' and resid 890 through 966)
42X-RAY DIFFRACTION42(chain 'g' and resid 890 through 966)
43X-RAY DIFFRACTION43(chain 'h' and resid 890 through 966)
44X-RAY DIFFRACTION44(chain 'i' and resid 890 through 966)
45X-RAY DIFFRACTION45(chain 'j' and resid 890 through 966)
46X-RAY DIFFRACTION46(chain 'k' and resid 890 through 966)
47X-RAY DIFFRACTION47(chain 'l' and resid 890 through 966)
48X-RAY DIFFRACTION48(chain 'm' and resid 890 through 966)
49X-RAY DIFFRACTION49(chain 'n' and resid 890 through 966)
50X-RAY DIFFRACTION50(chain 'o' and resid 890 through 966)
51X-RAY DIFFRACTION51(chain 'p' and resid 890 through 966)
52X-RAY DIFFRACTION52(chain 'q' and resid 890 through 966)
53X-RAY DIFFRACTION53(chain 'r' and resid 890 through 966)
54X-RAY DIFFRACTION54(chain 's' and resid 890 through 966)
55X-RAY DIFFRACTION55(chain 't' and resid 890 through 966)
56X-RAY DIFFRACTION56(chain 'u' and resid 890 through 966)
57X-RAY DIFFRACTION57(chain 'v' and resid 890 through 966)
58X-RAY DIFFRACTION58(chain 'w' and resid 890 through 966)
59X-RAY DIFFRACTION59(chain 'x' and resid 890 through 966)
60X-RAY DIFFRACTION60(chain 'y' and resid 890 through 966)

+
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