[English] 日本語
Yorodumi
- PDB-7ke3: Heavy chain ferritin with C-terminal EBNA1 epitope -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ke3
TitleHeavy chain ferritin with C-terminal EBNA1 epitope
ComponentsFerritin heavy chain,Epstein-Barr nuclear antigen 1
KeywordsOXIDOREDUCTASE / Protein nanoparticle / vaccine / virus like particle
Function / homology
Function and homology information


host cell PML body / viral latency / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / iron ion sequestering activity / symbiont-mediated disruption of host cell PML body / ferritin complex / negative regulation of ferroptosis / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase ...host cell PML body / viral latency / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / iron ion sequestering activity / symbiont-mediated disruption of host cell PML body / ferritin complex / negative regulation of ferroptosis / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / regulation of DNA replication / ferroxidase activity / enzyme-substrate adaptor activity / negative regulation of fibroblast proliferation / ferric iron binding / autophagosome / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / iron ion transport / endonuclease activity / symbiont-mediated suppression of host NF-kappaB cascade / ficolin-1-rich granule lumen / intracellular iron ion homeostasis / immune response / iron ion binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / Neutrophil degranulation / positive regulation of DNA-templated transcription / DNA binding / extracellular exosome / extracellular region / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Epstein Barr virus nuclear antigen-1, DNA-binding / Epstein Barr virus nuclear antigen-1, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / E2/EBNA1, C-terminal / Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin, core subunit, four-helix bundle / Ferritin ...Epstein Barr virus nuclear antigen-1, DNA-binding / Epstein Barr virus nuclear antigen-1, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / E2/EBNA1, C-terminal / Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Ferritin heavy chain / Epstein-Barr nuclear antigen 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Epstein-Barr virus (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsPederick, J.L. / Bruning, J.B.
CitationJournal: Vaccine / Year: 2021
Title: Immunogenicity study of engineered ferritins with C- and N-terminus insertion of Epstein-Barr nuclear antigen 1 epitope.
Authors: Qu, Y. / Zhang, B. / Wang, Y. / Yin, S. / Pederick, J.L. / Bruning, J.B. / Sun, Y. / Middelberg, A. / Bi, J.
History
DepositionOct 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
B: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
C: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
D: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
E: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
F: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
G: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
H: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
I: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
J: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
K: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
L: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,98038
Polymers282,13012
Non-polymers1,85026
Water12,809711
1
A: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
B: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
C: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
D: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
E: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
F: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
G: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
H: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
I: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
J: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
K: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
L: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
hetero molecules

A: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
B: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
C: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
D: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
E: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
F: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
G: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
H: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
I: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
J: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
K: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
L: Ferritin heavy chain,Epstein-Barr nuclear antigen 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)567,96076
Polymers564,26124
Non-polymers3,70052
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_777-y+2,-x+2,-z+21
Buried area97230 Å2
ΔGint-469 kcal/mol
Surface area130760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.882, 217.882, 147.203
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11C-304-

FE

21E-301-

FE

31C-450-

HOH

41E-455-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 23 through 48 or resid 50...
21(chain B and (resid 23 through 48 or resid 50...
31(chain C and (resid 23 through 48 or resid 50...
41(chain D and (resid 23 through 48 or resid 50...
51(chain E and (resid 23 through 48 or resid 50...
61(chain F and (resid 23 through 48 or resid 50...
71(chain G and (resid 23 through 48 or resid 50...
81(chain H and (resid 23 through 48 or resid 50...
91(chain I and (resid 23 through 48 or resid 50...
101(chain J and (resid 23 through 48 or resid 50...
111(chain K and (resid 23 through 48 or resid 50...
121(chain L and (resid 23 through 48 or resid 50...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 23 through 48 or resid 50...A23 - 48
121(chain A and (resid 23 through 48 or resid 50...A50 - 52
131(chain A and (resid 23 through 48 or resid 50...A53
141(chain A and (resid 23 through 48 or resid 50...A6 - 176
151(chain A and (resid 23 through 48 or resid 50...A6 - 176
161(chain A and (resid 23 through 48 or resid 50...A6 - 176
211(chain B and (resid 23 through 48 or resid 50...B23 - 48
221(chain B and (resid 23 through 48 or resid 50...B50 - 52
231(chain B and (resid 23 through 48 or resid 50...B53
241(chain B and (resid 23 through 48 or resid 50...B6 - 176
251(chain B and (resid 23 through 48 or resid 50...B6 - 176
261(chain B and (resid 23 through 48 or resid 50...B6 - 176
311(chain C and (resid 23 through 48 or resid 50...C23 - 48
321(chain C and (resid 23 through 48 or resid 50...C50 - 52
331(chain C and (resid 23 through 48 or resid 50...C53
341(chain C and (resid 23 through 48 or resid 50...C5 - 176
351(chain C and (resid 23 through 48 or resid 50...C5 - 176
361(chain C and (resid 23 through 48 or resid 50...C5 - 176
371(chain C and (resid 23 through 48 or resid 50...C5 - 176
381(chain C and (resid 23 through 48 or resid 50...C5 - 176
391(chain C and (resid 23 through 48 or resid 50...C5 - 176
411(chain D and (resid 23 through 48 or resid 50...D23 - 48
421(chain D and (resid 23 through 48 or resid 50...D50 - 52
431(chain D and (resid 23 through 48 or resid 50...D53
441(chain D and (resid 23 through 48 or resid 50...D6 - 176
451(chain D and (resid 23 through 48 or resid 50...D6 - 176
461(chain D and (resid 23 through 48 or resid 50...D6 - 176
511(chain E and (resid 23 through 48 or resid 50...E23 - 48
521(chain E and (resid 23 through 48 or resid 50...E50 - 52
531(chain E and (resid 23 through 48 or resid 50...E53
541(chain E and (resid 23 through 48 or resid 50...E5 - 176
551(chain E and (resid 23 through 48 or resid 50...E5 - 176
561(chain E and (resid 23 through 48 or resid 50...E5 - 176
571(chain E and (resid 23 through 48 or resid 50...E5 - 176
581(chain E and (resid 23 through 48 or resid 50...E5 - 176
611(chain F and (resid 23 through 48 or resid 50...F23 - 48
621(chain F and (resid 23 through 48 or resid 50...F50 - 60
631(chain F and (resid 23 through 48 or resid 50...F62
641(chain F and (resid 23 through 48 or resid 50...F65 - 67
651(chain F and (resid 23 through 48 or resid 50...F88 - 101
661(chain F and (resid 23 through 48 or resid 50...F5 - 176
671(chain F and (resid 23 through 48 or resid 50...F5 - 176
681(chain F and (resid 23 through 48 or resid 50...F5 - 176
691(chain F and (resid 23 through 48 or resid 50...F5 - 176
6101(chain F and (resid 23 through 48 or resid 50...F5 - 176
6111(chain F and (resid 23 through 48 or resid 50...F5 - 176
711(chain G and (resid 23 through 48 or resid 50...G23 - 48
721(chain G and (resid 23 through 48 or resid 50...G50 - 52
731(chain G and (resid 23 through 48 or resid 50...G53
741(chain G and (resid 23 through 48 or resid 50...G5 - 176
751(chain G and (resid 23 through 48 or resid 50...G5 - 176
761(chain G and (resid 23 through 48 or resid 50...G5 - 176
771(chain G and (resid 23 through 48 or resid 50...G5 - 176
781(chain G and (resid 23 through 48 or resid 50...G5 - 176
811(chain H and (resid 23 through 48 or resid 50...H23 - 48
821(chain H and (resid 23 through 48 or resid 50...H50 - 52
831(chain H and (resid 23 through 48 or resid 50...H53
841(chain H and (resid 23 through 48 or resid 50...H5 - 176
851(chain H and (resid 23 through 48 or resid 50...H5 - 176
861(chain H and (resid 23 through 48 or resid 50...H5 - 176
871(chain H and (resid 23 through 48 or resid 50...H5 - 176
881(chain H and (resid 23 through 48 or resid 50...H5 - 176
911(chain I and (resid 23 through 48 or resid 50...I23 - 48
921(chain I and (resid 23 through 48 or resid 50...I50 - 60
931(chain I and (resid 23 through 48 or resid 50...I62
941(chain I and (resid 23 through 48 or resid 50...I0
951(chain I and (resid 23 through 48 or resid 50...I5 - 176
961(chain I and (resid 23 through 48 or resid 50...I5 - 176
971(chain I and (resid 23 through 48 or resid 50...I5 - 176
981(chain I and (resid 23 through 48 or resid 50...I5 - 176
991(chain I and (resid 23 through 48 or resid 50...I5 - 176
9101(chain I and (resid 23 through 48 or resid 50...I5 - 176
9111(chain I and (resid 23 through 48 or resid 50...I5 - 176
1011(chain J and (resid 23 through 48 or resid 50...J23 - 48
1021(chain J and (resid 23 through 48 or resid 50...J50 - 52
1031(chain J and (resid 23 through 48 or resid 50...J53
1041(chain J and (resid 23 through 48 or resid 50...J5 - 176
1051(chain J and (resid 23 through 48 or resid 50...J5 - 176
1061(chain J and (resid 23 through 48 or resid 50...J5 - 176
1111(chain K and (resid 23 through 48 or resid 50...K23 - 48
1121(chain K and (resid 23 through 48 or resid 50...K50 - 52
1131(chain K and (resid 23 through 48 or resid 50...K53
1141(chain K and (resid 23 through 48 or resid 50...K5 - 176
1151(chain K and (resid 23 through 48 or resid 50...K5 - 176
1161(chain K and (resid 23 through 48 or resid 50...K5 - 176
1171(chain K and (resid 23 through 48 or resid 50...K5 - 176
1181(chain K and (resid 23 through 48 or resid 50...K5 - 176
1211(chain L and (resid 23 through 48 or resid 50...L23 - 48
1221(chain L and (resid 23 through 48 or resid 50...L50 - 52
1231(chain L and (resid 23 through 48 or resid 50...L53
1241(chain L and (resid 23 through 48 or resid 50...L5 - 176
1251(chain L and (resid 23 through 48 or resid 50...L5 - 176
1261(chain L and (resid 23 through 48 or resid 50...L5 - 176
1271(chain L and (resid 23 through 48 or resid 50...L5 - 176
1281(chain L and (resid 23 through 48 or resid 50...L5 - 176
1291(chain L and (resid 23 through 48 or resid 50...L5 - 176

-
Components

#1: Protein
Ferritin heavy chain,Epstein-Barr nuclear antigen 1 / Ferritin H subunit / Cell proliferation-inducing gene 15 protein / EBV nuclear antigen 1


Mass: 23510.867 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15, EBNA1, BKRF1 / Strain: B95-8 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P02794, UniProt: P03211, ferroxidase
#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 711 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.27 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH 7.0, 30% Jeffamine M-600 pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→48.72 Å / Num. obs: 177978 / % possible obs: 99.9 % / Redundancy: 27.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.336 / Rpim(I) all: 0.065 / Rrim(I) all: 0.342 / Net I/σ(I): 8.9 / Num. measured all: 4871537
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.2427.62.54924013187030.9070.4932.5971.699.8
12.05-48.7225.20.05631305124110.0120.05729.898.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8.38 Å48.72 Å
Translation8.38 Å48.72 Å

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.18.2-3874refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J4A

6j4a


Resolution: 2.2→48.72 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2705 8841 5.01 %
Rwork0.2407 167570 -
obs0.2422 176411 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.63 Å2 / Biso mean: 26.4795 Å2 / Biso min: 15.41 Å2
Refinement stepCycle: final / Resolution: 2.2→48.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16158 0 68 711 16937
Biso mean--33.46 31.71 -
Num. residues----2001
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7885X-RAY DIFFRACTION7.108TORSIONAL
12B7885X-RAY DIFFRACTION7.108TORSIONAL
13C7885X-RAY DIFFRACTION7.108TORSIONAL
14D7885X-RAY DIFFRACTION7.108TORSIONAL
15E7885X-RAY DIFFRACTION7.108TORSIONAL
16F7885X-RAY DIFFRACTION7.108TORSIONAL
17G7885X-RAY DIFFRACTION7.108TORSIONAL
18H7885X-RAY DIFFRACTION7.108TORSIONAL
19I7885X-RAY DIFFRACTION7.108TORSIONAL
110J7885X-RAY DIFFRACTION7.108TORSIONAL
111K7885X-RAY DIFFRACTION7.108TORSIONAL
112L7885X-RAY DIFFRACTION7.108TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.230.32172940.28595522581699
2.23-2.250.37642760.35795463573998
2.25-2.280.35233030.32195415571898
2.28-2.310.32562670.27095574584199
2.31-2.340.30843100.257455425852100
2.34-2.370.28952830.2515587587099
2.37-2.40.27412780.249655425820100
2.4-2.440.282840.255155765860100
2.44-2.480.29132930.24455735866100
2.48-2.520.26242670.23855935860100
2.52-2.560.27443290.23755485877100
2.56-2.610.25742820.237555835865100
2.61-2.660.26282860.227156015887100
2.66-2.710.24982810.22755589587099
2.71-2.770.23953090.23645556586599
2.77-2.840.25032970.22815551584899
2.84-2.910.25052980.23025585588399
2.91-2.990.26332930.22685589588299
2.99-3.070.27743010.22955580588199
3.07-3.170.26622740.21185605587999
3.17-3.290.22613260.21745593591999
3.29-3.420.24662920.22045619591199
3.42-3.570.22862790.22575592587199
3.57-3.760.27792890.22925586587598
3.76-40.26432900.225607589799
4-4.310.25992980.21765645594399
4.31-4.740.22743270.21935620594799
4.74-5.420.28143170.255612592998
5.42-6.830.35323210.291957646085100
6.83-48.720.27082970.26275758605595
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)
10.75-0.18510.12161.834-1.96321.22830.1330.0354-0.10070.11960.16260.4243-0.2369-0.2054-0.17290.235-0.0190.02080.2062-0.04810.218222.7324159.9763158.033
20.24771.1292-0.67244.2458-2.09522.021-0.08980.0766-0.0806-0.0760.0132-0.45670.08680.06940.08390.17930.0223-0.01080.3024-0.01470.2931230.7068167.4572150.7484
31.62550.20141.16521.9441-0.90841.60650.1853-0.1469-0.2049-0.23250.20230.61050.0243-0.2741-0.32570.2427-0.0120.06510.3459-0.02390.2687219.259158.5068154.3104
40.37291.5349-0.95074.0477-2.03551.77720.1738-0.10760.06880.0893-0.04830.4131-0.1658-0.1185-0.01650.18110.0250.03560.2791-0.04860.2957224.9446166.5658165.9341
50.671.1712-1.83591.4302-2.50064.4541-0.0921-0.12180.1151-0.0101-0.1465-0.2528-0.02910.07560.17790.2269-0.0078-0.02480.242-0.05790.2339232.998183.9013155.0022
66.51234.1769-1.89693.2632-0.80971.3828-0.72360.3983-0.9886-0.7971-0.1923-1.0226-0.0631-0.10410.36170.13880.0453-0.16630.19430.19610.1882223.7734177.2122124.8195
71.137-0.96330.53683.6505-2.57591.59880.17070.1927-0.0895-0.2561-0.05840.40920.25460.0974-0.12580.22040.0064-0.00840.2097-0.02260.2689223.5393154.3831143.3475
80.6078-2.66490.40929.0628-5.42384.2641-0.16790.06090.2115-0.0851-0.2063-0.83260.04340.15010.34330.1973-0.0211-0.02360.1915-0.00540.2331231.2824157.6888141.038
91.5226-0.538-1.36141.8936-0.33491.56080.2245-0.09120.09260.3620.31410.4926-0.2772-0.3216-0.53750.2242-0.1098-0.05730.2868-0.04060.2146219.4358163.5632140.3869
100.9608-1.70331.37878.6886-6.34896.45370.2267-0.1128-0.2949-0.39550.40721.00780.2512-0.126-0.58510.21880.0351-0.01320.2911-0.01410.269222.6414150.8568131.3585
116.858-1.75492.83663.4424-1.24934.04540.20681.1897-0.1807-0.3049-0.0972-0.21310.22041.0748-0.08320.33010.0305-0.04480.3228-0.01480.2461229.0617164.2369123.4954
121.8902-2.03671.35346.7432-3.58173.60410.1745-0.10890.43490.5047-0.6014-0.4843-0.15050.58310.35720.17410.0149-0.02590.31010.00890.2475231.8235142.052134.052
135.26422.15352.39813.5104-0.98157.45020.31-1.1122-0.68720.32390.0030.2743-0.3861-0.7062-0.4220.28170.01550.01150.31160.01430.3105227.0071129.1072145.5309
141.420.1460.05254.2252-2.07354.7681-0.0174-0.1160.0957-0.02970.0788-0.1735-0.0218-0.2732-0.13230.28830.09530.00570.27450.00730.1348236.7752135.1149147.0149
152.7342-2.4477-0.16162.34120.93262.6354-0.13410.11550.0540.31610.17930.29720.04850.27760.04960.3031-0.0578-0.01350.1863-0.00940.1723257.9205109.7357125.1721
162.69040.20282.13171.1611-0.14541.82360.2121-0.0386-0.19250.09310.0058-0.00630.20070.0335-0.16470.26950.01240.06570.2511-0.02770.212281.3708109.8867143.3157
177.53052.40564.11840.38911.17213.3229-0.3063-0.07660.8163-0.02-0.06720.2671-0.2348-0.1340.31350.25880.03220.02040.19040.00350.3232278.0068117.5657141.0631
181.94751.15060.33030.6842-0.98421.1042-0.1307-0.059-0.590.04940.25860.15040.0047-0.2559-0.13640.2121-0.0170.00560.2507-0.08670.3227272.1774105.7761140.3973
195.03990.9892.64790.76681.24022.4978-0.09150.1666-0.2019-0.15720.071-0.05610.07080.1926-0.00640.2687-0.00720.08430.1558-0.02290.2464280.143111.2454128.5683
202.08921.24832.43860.84081.06683.8003-0.05290.05240.17440.0256-0.1188-0.2685-0.06330.02510.12530.28180.00480.05550.2350.01880.2842297.7989119.0869139.4623
211.42650.5066-0.39561.8170.46820.3304-0.08760.07090.0631-0.2242-0.09730.25010.06020.36990.33150.1870.0066-0.06510.35120.08650.334290.9281110.1339169.7949
223.4939-0.48442.85010.3839-0.20482.38240.075-0.116-0.55280.04310.18320.1301-0.0771-0.0861-0.24960.19580.00140.03870.16440.00940.2484268.0461109.9161151.2984
237.6473-2.54253.7725-0.0017-0.87052.1162-0.3096-0.09190.47410.0161-0.0524-0.2445-0.2525-0.07510.39410.23110.01840.01030.20280.00190.2865271.2155117.7156153.7024
241.5221-1.0677-1.55971.59811.31921.6409-0.23810.3193-0.497-0.15390.1860.03320.03050.8305-0.14470.3016-0.09720.0813-0.01210.04930.2992277.1973105.7783154.1975
256.9317-1.49916.03970.6168-1.50495.54330.107-0.4572-0.8093-0.14340.29110.1518-0.2447-0.3939-0.46060.29370.03460.0150.26410.00770.2729264.4187109.0881163.0219
263.5876-0.54050.47211.93390.2442.4953-0.1675-0.22840.16160.4171-0.00820.0431-0.2038-0.04070.13840.34180.03440.04890.29680.06150.2694277.9885115.4197171.1132
271.5774-1.53731.18680.6026-1.44552.3031-0.03740.2825-0.1726-0.1250.0335-0.1727-0.15940.00830.04520.25930.0220.00750.16830.00260.1783251.5511119.1909155.0904
281.6273-1.16520.3611.11610.10151.4891-0.6750.68040.07330.43170.0578-0.14370.75270.2423-0.05590.4086-0.0153-0.27310.376-0.08620.1596241.5611162.550999.087
290.590.53510.65861.64851.26162.173-0.0326-0.00610.0873-0.2365-0.05270.1511-0.1825-0.09250.1370.1730.0074-0.01480.19450.03640.2523243.0324187.3404116.0112
300.14480.5225-0.71994.94515.85516.83220.14390.0334-0.04450.15360.1027-0.26820.23410.0879-0.20890.22830.06620.0160.25720.01760.2465246.8102179.9299118.8409
310.00080.4914-0.60941.6165-0.28141.4193-0.0192-0.023-0.0479-0.7191-0.0359-0.1293-0.2947-0.11250.12560.16940.0371-0.03420.27650.01090.1715243.0517183.231106.9888
321.0770.81441.20073.53633.10742.61340.1145-0.02310.1661-0.0021-0.22390.34520.0384-0.29470.09840.22290.02860.02680.27150.05640.1847233.8391175.4871115.9211
331.53141.93851.72822.99851.94733.1114-0.0157-0.00550.12170.02190.12440.0784-0.05680.0649-0.18370.20680.0164-0.00240.2360.05040.2342236.8731187.8233133.8645
341.41591.6126-1.26111.824-1.05276.19250.27310.420.62880.4170.27310.20130.1177-0.2469-0.3940.29620.0597-0.03450.21660.05090.3676256.3501210.6843122.7467
350.4297-0.21280.08933.17321.12530.3634-0.04640.1056-0.0259-0.37480.0960.2147-0.0791-0.0712-0.07040.2796-0.0276-0.00110.2610.02990.1881255.2118185.6285106.1625
360.8407-1.5315-1.41017.39555.63953.4336-0.096-0.18960.12680.496-0.0058-0.25570.2350.10980.09810.21720.0085-0.07120.27630.02380.1638259.0492185.9491114.2261
372.8775-0.6658-0.20512.3352.78413.17690.2020.01760.13-0.2208-0.73880.2012-0.2781-0.91450.35330.32220.0132-0.03640.24860.11490.2323250.6167194.7447109.8451
38-0.0966-0.3896-0.32464.57572.31132.44590.17470.0540.0196-0.3109-0.0423-0.2616-0.1947-0.1527-0.08720.1593-0.01340.01010.20180.02170.2109265.743196.3497108.0469
390.87690.6878-0.44054.76721.76720.91910.07640.20260.07050.085-0.28280.21870.125-0.22030.18960.2233-0.0226-0.03790.27860.01630.2985270.7121175.742101.4669
401.2883-0.82572.1870.6355-1.10656.9111-0.09040.23070.350.19380.12050.3225-0.3903-0.0787-0.21230.17410.04360.03670.19330.07020.2363256.4542111.4547171.7705
41-0.02650.58590.2353.71982.10811.02030.11070.0083-0.03340.4457-0.1647-0.20270.1605-0.16720.05170.1813-0.0022-0.00510.22830.02390.2221255.4336136.4932188.309
421.18691.31580.58275.41695.50432.9964-0.230.0980.0241-0.90240.4971-0.1219-0.30410.4555-0.20410.339-0.0088-0.02430.260.00970.2145259.3057135.8233179.9226
433.5197-0.485-1.1210.53060.15881.17570.1309-0.0647-0.26530.2173-0.27540.01070.0366-0.81920.30970.24180.0383-0.010.23210.05950.157249.8734128.6084186.0149
440.02740.33970.68064.49762.62361.50440.1137-0.0123-0.0585-0.0173-0.0404-0.249-0.0299-0.1375-0.05240.2711-0.0502-0.01540.25140.04760.2058265.9173125.7699186.3652
450.2094-1.30410.20275.20540.39140.1746-0.00960.03820.06860.06050.04150.0073-0.12870.017-0.06630.1924-0.03960.01940.22630.03710.2464270.9058146.2218192.9861
468.71072.7579-2.78095.037-1.56630.9499-0.445-1.2683-0.39010.4435-0.4742-0.0932-0.1799-0.1310.57080.3324-0.0547-0.0060.2036-0.04290.2558241.9376159.5472195.444
470.4363-0.5348-0.24432.35431.94822.03710.07030.184-0.02780.217-0.2017-0.03690.3476-0.04190.110.20080.01910.00570.25860.00820.2368241.9599137.9909181.6062
483.8869-0.4592-1.19772.4578-2.63723.6334-0.4685-0.3742-0.4251-0.72340.1246-0.21010.34030.12630.09670.40820.00740.02320.2944-0.03470.2655248.1502121.3494165.822
490.2558-0.11040.92924.86755.11346.2006-0.13050.08090.15540.56150.16780.17060.48780.3852-0.09670.2361-0.05640.05770.23390.02430.2149246.9749142.1454175.7793
501.1529-0.01560.3430.4463-0.94881.92510.3767-0.5795-0.1346-0.1505-0.5608-0.16020.1191-0.33050.10260.3306-0.01920.00940.30150.02910.2547243.5476139.6432188.2094
511.5326-0.7686-1.87445.42214.39934.70310.2048-0.0544-0.09050.3342-0.23570.0760.1904-0.39970.1040.19150.0395-0.02210.23250.04420.218232.4534141.1153176.9961
522.4823-0.56070.7654.21441.62342.82770.0562-0.17570.6373-0.12950.1708-0.5971-0.32680.4919-0.15830.19720.00890.01180.3351-0.030.26236.8068156.6462181.9593
530.7979-1.0411-1.11112.66582.76252.28540.0317-0.0336-0.0517-0.11540.0056-0.0071-0.1006-0.04820.00620.23610.0389-0.00430.24280.05040.174236.991134.4034160.7307
541.5346-0.3139-1.42020.2330.12030.8277-0.0360.1184-0.1445-0.0184-0.0705-0.04670.0455-0.03440.09910.2710.0057-0.05350.2419-0.01630.294240.0572141.7841111.6233
553.4817-0.1729-2.97371.2387-0.87771.96990.25540.32320.00360.0596-0.0330.0003-0.2282-0.366-0.15870.237-0.0326-0.04250.2637-0.00760.1734253.433144.2373111.6152
560.96290.2928-1.01982.72911.0370.6554-0.03720.5674-0.3275-0.1681-0.11050.2463-0.0101-0.42280.23020.35220.0562-0.02850.35010.00240.137240.62136.8425109.9232
573.7065-0.1924-1.71951.2641-0.2682.0231-0.075-0.00060.12910.06020.12610.04480.0694-0.1061-0.06270.2666-0.0325-0.05930.21550.02210.1821239.2803151.9712108.1964
585.0928-0.4781-1.23580.7262-0.19990.5497-0.009-0.14850.1193-0.01880.0439-0.07020.1540.0558-0.06260.2299-0.03-0.03680.2258-0.02060.1734259.5189156.9638101.7383
592.3454-0.1036-1.01440.55250.20731.5499-0.24290.2251-0.3271-0.00180.07680.04690.2185-0.17540.11660.24770.00060.00170.2008-0.01160.2172257.0587128.0168109.3193
603.8406-0.5754-4.29810.2728-0.02584.09750.24710.08560.18580.0001-0.0449-0.0781-0.20380.0802-0.19130.2019-0.0185-0.02340.2382-0.04320.198251.8367133.3872120.8089
611.36290.09461.12871.2066-1.03111.6396-0.58390.00370.6777-0.4880.61230.34960.6102-0.0776-0.08650.2713-0.0514-0.00040.2566-0.05080.2078253.0853129.6371106.4027
623.4016-0.4993-3.32631.06980.16973.065-0.17790.18560.0733-0.25560.0943-0.03010.2169-0.18620.06410.29580.0201-0.00830.2315-0.03590.1952260.1723120.1188115.9245
632.7905-1.8429-1.85591.30771.66112.3653-0.0418-0.2453-0.2005-0.022-0.03820.01760.01060.02940.07710.24330.0115-0.04660.2271-0.00090.1639247.8628123.2154133.9654
643.9393-1.4916-1.1961.7730.74932.966-0.21330.38280.043-0.79240.0562-0.1346-0.3649-0.84310.00280.265-0.18610.12740.3092-0.04350.2157307.4806159.335298.9755
650.88040.7298-1.11043.0686-1.62112.3223-0.0405-0.0487-0.2447-0.2022-0.1295-0.2367-0.03010.17110.18270.19490.00840.00690.2187-0.0210.2304307.624138.0797112.5746
660.23980.256-0.50392.8676-3.0212.162-0.0629-0.0187-0.0616-0.0540.015-0.08260.0198-0.1844-0.01520.2645-0.01250.01820.2118-0.02910.2652302.4194138.6874120.057
67-0.48990.25770.55421.53241.24021.1220.10010.1764-0.0775-0.6269-0.05490.08390.50180.23290.1310.18460.05470.03330.3549-0.02420.2751305.883137.455106.2384
680.45130.2828-0.58872.9419-2.54043.54540.0568-0.0996-0.01080.0691-0.1144-0.052-0.1310.20710.13820.1620.02050.00530.2897-0.03310.2355315.4495146.498115.761
691.31051.3422-1.07943.1667-2.80022.8131-0.0136-0.06750.062-0.01850.07490.15780.12170.018-0.14190.2490.01980.02910.2545-0.04840.3267312.518134.2355133.7684
701.0180.3713-0.03121.4687-0.29270.9581-0.06870.1143-0.0812-0.18290.0827-0.07310.1425-0.05040.00760.27260.02140.05620.2579-0.02580.1783293.8049126.404111.5354
710.7757-0.870.3353.5827-3.26541.744-0.034-0.12650.03420.0593-0.092-0.0222-0.1180.110.10520.2918-0.02770.02730.2028-0.04880.1898291.1055140.0501111.3282
722.06940.2805-1.01931.3417-0.8722.2161-0.0280.048-0.0868-0.134-0.328-0.26260.18630.47160.16350.25280.0180.02120.2203-0.08070.1537298.6931127.1895109.8723
73-0.0325-0.0443-0.04433.8223-1.44211.50170.0761-0.0115-0.0129-0.0578-0.1849-0.02570.03470.10460.0920.1888-0.03420.01690.2308-0.03710.2494283.6763125.6035108.1755
740.53340.40930.55454.5087-0.89330.6030.03670.2181-0.19670.3011-0.1393-0.1275-0.18330.18110.07120.2436-0.05470.08040.2668-0.03830.2841278.6341145.9466101.6598
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 41 )A6 - 41
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 75 )A42 - 75
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 95 )A76 - 95
4X-RAY DIFFRACTION4chain 'A' and (resid 96 through 137 )A96 - 137
5X-RAY DIFFRACTION5chain 'A' and (resid 138 through 176 )A138 - 176
6X-RAY DIFFRACTION6chain 'B' and (resid 6 through 13 )B6 - 13
7X-RAY DIFFRACTION7chain 'B' and (resid 14 through 48 )B14 - 48
8X-RAY DIFFRACTION8chain 'B' and (resid 49 through 75 )B49 - 75
9X-RAY DIFFRACTION9chain 'B' and (resid 76 through 95 )B76 - 95
10X-RAY DIFFRACTION10chain 'B' and (resid 96 through 123 )B96 - 123
11X-RAY DIFFRACTION11chain 'B' and (resid 124 through 137 )B124 - 137
12X-RAY DIFFRACTION12chain 'B' and (resid 138 through 158 )B138 - 158
13X-RAY DIFFRACTION13chain 'B' and (resid 159 through 163 )B159 - 163
14X-RAY DIFFRACTION14chain 'B' and (resid 164 through 176 )B164 - 176
15X-RAY DIFFRACTION15chain 'C' and (resid 5 through 13 )C5 - 13
16X-RAY DIFFRACTION16chain 'C' and (resid 14 through 48 )C14 - 48
17X-RAY DIFFRACTION17chain 'C' and (resid 49 through 75 )C49 - 75
18X-RAY DIFFRACTION18chain 'C' and (resid 76 through 95 )C76 - 95
19X-RAY DIFFRACTION19chain 'C' and (resid 96 through 137 )C96 - 137
20X-RAY DIFFRACTION20chain 'C' and (resid 138 through 176 )C138 - 176
21X-RAY DIFFRACTION21chain 'D' and (resid 6 through 13 )D6 - 13
22X-RAY DIFFRACTION22chain 'D' and (resid 14 through 48 )D14 - 48
23X-RAY DIFFRACTION23chain 'D' and (resid 49 through 75 )D49 - 75
24X-RAY DIFFRACTION24chain 'D' and (resid 76 through 95 )D76 - 95
25X-RAY DIFFRACTION25chain 'D' and (resid 96 through 123 )D96 - 123
26X-RAY DIFFRACTION26chain 'D' and (resid 124 through 137 )D124 - 137
27X-RAY DIFFRACTION27chain 'D' and (resid 138 through 176 )D138 - 176
28X-RAY DIFFRACTION28chain 'E' and (resid 5 through 13 )E5 - 13
29X-RAY DIFFRACTION29chain 'E' and (resid 14 through 48 )E14 - 48
30X-RAY DIFFRACTION30chain 'E' and (resid 49 through 75 )E49 - 75
31X-RAY DIFFRACTION31chain 'E' and (resid 76 through 95 )E76 - 95
32X-RAY DIFFRACTION32chain 'E' and (resid 96 through 137 )E96 - 137
33X-RAY DIFFRACTION33chain 'E' and (resid 138 through 176 )E138 - 176
34X-RAY DIFFRACTION34chain 'F' and (resid 5 through 13 )F5 - 13
35X-RAY DIFFRACTION35chain 'F' and (resid 14 through 48 )F14 - 48
36X-RAY DIFFRACTION36chain 'F' and (resid 49 through 75 )F49 - 75
37X-RAY DIFFRACTION37chain 'F' and (resid 76 through 95 )F76 - 95
38X-RAY DIFFRACTION38chain 'F' and (resid 96 through 137 )F96 - 137
39X-RAY DIFFRACTION39chain 'F' and (resid 138 through 176 )F138 - 176
40X-RAY DIFFRACTION40chain 'G' and (resid 5 through 13 )G5 - 13
41X-RAY DIFFRACTION41chain 'G' and (resid 14 through 48 )G14 - 48
42X-RAY DIFFRACTION42chain 'G' and (resid 49 through 76 )G49 - 76
43X-RAY DIFFRACTION43chain 'G' and (resid 77 through 95 )G77 - 95
44X-RAY DIFFRACTION44chain 'G' and (resid 96 through 137 )G96 - 137
45X-RAY DIFFRACTION45chain 'G' and (resid 138 through 176 )G138 - 176
46X-RAY DIFFRACTION46chain 'H' and (resid 5 through 13 )H5 - 13
47X-RAY DIFFRACTION47chain 'H' and (resid 14 through 41 )H14 - 41
48X-RAY DIFFRACTION48chain 'H' and (resid 42 through 48 )H42 - 48
49X-RAY DIFFRACTION49chain 'H' and (resid 49 through 75 )H49 - 75
50X-RAY DIFFRACTION50chain 'H' and (resid 76 through 95 )H76 - 95
51X-RAY DIFFRACTION51chain 'H' and (resid 96 through 123 )H96 - 123
52X-RAY DIFFRACTION52chain 'H' and (resid 124 through 137 )H124 - 137
53X-RAY DIFFRACTION53chain 'H' and (resid 138 through 176 )H138 - 176
54X-RAY DIFFRACTION54chain 'I' and (resid 5 through 41 )I5 - 41
55X-RAY DIFFRACTION55chain 'I' and (resid 42 through 75 )I42 - 75
56X-RAY DIFFRACTION56chain 'I' and (resid 76 through 95 )I76 - 95
57X-RAY DIFFRACTION57chain 'I' and (resid 96 through 137 )I96 - 137
58X-RAY DIFFRACTION58chain 'I' and (resid 138 through 176 )I138 - 176
59X-RAY DIFFRACTION59chain 'J' and (resid 5 through 41 )J5 - 41
60X-RAY DIFFRACTION60chain 'J' and (resid 42 through 75 )J42 - 75
61X-RAY DIFFRACTION61chain 'J' and (resid 76 through 95 )J76 - 95
62X-RAY DIFFRACTION62chain 'J' and (resid 96 through 137 )J96 - 137
63X-RAY DIFFRACTION63chain 'J' and (resid 138 through 176 )J138 - 176
64X-RAY DIFFRACTION64chain 'K' and (resid 5 through 13 )K5 - 13
65X-RAY DIFFRACTION65chain 'K' and (resid 14 through 41 )K14 - 41
66X-RAY DIFFRACTION66chain 'K' and (resid 42 through 76 )K42 - 76
67X-RAY DIFFRACTION67chain 'K' and (resid 77 through 95 )K77 - 95
68X-RAY DIFFRACTION68chain 'K' and (resid 96 through 137 )K96 - 137
69X-RAY DIFFRACTION69chain 'K' and (resid 138 through 176 )K138 - 176
70X-RAY DIFFRACTION70chain 'L' and (resid 5 through 41 )L5 - 41
71X-RAY DIFFRACTION71chain 'L' and (resid 42 through 75 )L42 - 75
72X-RAY DIFFRACTION72chain 'L' and (resid 76 through 95 )L76 - 95
73X-RAY DIFFRACTION73chain 'L' and (resid 96 through 137 )L96 - 137
74X-RAY DIFFRACTION74chain 'L' and (resid 138 through 176 )L138 - 176

+
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