[English] 日本語
Yorodumi
- PDB-7yz8: Triclinic crystal structure of YTHDF1 YTH domain (544AVV546 mutant) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yz8
TitleTriclinic crystal structure of YTHDF1 YTH domain (544AVV546 mutant)
ComponentsYTH domain-containing family protein 1
KeywordsRNA BINDING PROTEIN / mRNA binding and stability
Function / homology
Function and homology information


regulation of axon guidance / organelle assembly / regulation of antigen processing and presentation / N6-methyladenosine-containing RNA reader activity / regulation of long-term synaptic potentiation / mRNA destabilization / positive regulation of translational initiation / immune system process / regulation of mRNA stability / stress granule assembly ...regulation of axon guidance / organelle assembly / regulation of antigen processing and presentation / N6-methyladenosine-containing RNA reader activity / regulation of long-term synaptic potentiation / mRNA destabilization / positive regulation of translational initiation / immune system process / regulation of mRNA stability / stress granule assembly / learning / positive regulation of translation / P-body / memory / cytoplasmic stress granule / ribosome binding / mRNA binding / RNA binding / cytoplasm
Similarity search - Function
YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile.
Similarity search - Domain/homology
THIOCYANATE ION / YTH domain-containing family protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsDalle Vedove, A. / Cazzanelli, G. / Lolli, G.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchMFAG 2017 - ID. 19882 Italy
CitationJournal: J.Chem.Inf.Model. / Year: 2024
Title: Pliability in the m 6 A-Binding Region Extends Druggability of YTH Domains.
Authors: Cazzanelli, G. / Dalle Vedove, A. / Spagnolli, G. / Terruzzi, L. / Colasurdo, E. / Boldrini, A. / Patsilinakos, A. / Sturlese, M. / Grottesi, A. / Biasini, E. / Provenzani, A. / Quattrone, A. / Lolli, G.
History
DepositionFeb 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Mar 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: YTH domain-containing family protein 1
B: YTH domain-containing family protein 1
C: YTH domain-containing family protein 1
D: YTH domain-containing family protein 1
E: YTH domain-containing family protein 1
F: YTH domain-containing family protein 1
G: YTH domain-containing family protein 1
H: YTH domain-containing family protein 1
I: YTH domain-containing family protein 1
J: YTH domain-containing family protein 1
K: YTH domain-containing family protein 1
L: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,47524
Polymers277,77812
Non-polymers69712
Water5,459303
1
A: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2062
Polymers23,1481
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2062
Polymers23,1481
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2062
Polymers23,1481
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2062
Polymers23,1481
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2062
Polymers23,1481
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2062
Polymers23,1481
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2062
Polymers23,1481
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2062
Polymers23,1481
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2062
Polymers23,1481
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2062
Polymers23,1481
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2062
Polymers23,1481
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: YTH domain-containing family protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2062
Polymers23,1481
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.225, 92.571, 113.940
Angle α, β, γ (deg.)72.870, 79.050, 67.870
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))
21(chain B and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))
31(chain C and (resid 366 through 396 or resid 398 through 557))
41(chain D and (resid 366 through 396 or resid 398 through 557))
51(chain E and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))
61(chain F and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))
71(chain G and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))
81(chain H and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))
91(chain I and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))
101(chain J and (resid 366 through 396 or resid 398 through 557))
111(chain K and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))
121(chain L and (resid 366 through 396 or resid 398 through 557))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROSERSER(chain A and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))AA366 - 3967 - 37
12SERSERTYRTYR(chain A and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))AA398 - 45839 - 99
13TRPTRPASNASN(chain A and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))AA470 - 557111 - 198
21PROPROSERSER(chain B and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))BB366 - 3967 - 37
22SERSERTYRTYR(chain B and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))BB398 - 45839 - 99
23TRPTRPASNASN(chain B and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))BB470 - 557111 - 198
31PROPROSERSER(chain C and (resid 366 through 396 or resid 398 through 557))CC366 - 3967 - 37
32SERSERASNASN(chain C and (resid 366 through 396 or resid 398 through 557))CC398 - 55739 - 198
41PROPROSERSER(chain D and (resid 366 through 396 or resid 398 through 557))DD366 - 3967 - 37
42SERSERASNASN(chain D and (resid 366 through 396 or resid 398 through 557))DD398 - 55739 - 198
51PROPROSERSER(chain E and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))EE366 - 3967 - 37
52SERSERTYRTYR(chain E and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))EE398 - 45839 - 99
53TRPTRPASNASN(chain E and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))EE470 - 557111 - 198
61PROPROSERSER(chain F and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))FF366 - 3967 - 37
62SERSERTYRTYR(chain F and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))FF398 - 45839 - 99
63TRPTRPASNASN(chain F and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))FF470 - 557111 - 198
71PROPROSERSER(chain G and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))GG366 - 3967 - 37
72SERSERTYRTYR(chain G and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))GG398 - 45839 - 99
73TRPTRPASNASN(chain G and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))GG470 - 557111 - 198
81PROPROSERSER(chain H and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))HH366 - 3967 - 37
82SERSERTYRTYR(chain H and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))HH398 - 45839 - 99
83TRPTRPASNASN(chain H and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))HH470 - 557111 - 198
91PROPROSERSER(chain I and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))II366 - 3967 - 37
92SERSERTYRTYR(chain I and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))II398 - 45839 - 99
93TRPTRPASNASN(chain I and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))II470 - 557111 - 198
101PROPROSERSER(chain J and (resid 366 through 396 or resid 398 through 557))JJ366 - 3967 - 37
102SERSERASNASN(chain J and (resid 366 through 396 or resid 398 through 557))JJ398 - 55739 - 198
111PROPROSERSER(chain K and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))KK366 - 3967 - 37
112SERSERTYRTYR(chain K and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))KK398 - 45839 - 99
113TRPTRPASNASN(chain K and (resid 366 through 396 or resid 398 through 458 or resid 470 through 557))KK470 - 557111 - 198
121PROPROSERSER(chain L and (resid 366 through 396 or resid 398 through 557))LL366 - 3967 - 37
122SERSERASNASN(chain L and (resid 366 through 396 or resid 398 through 557))LL398 - 55739 - 198

-
Components

#1: Protein
YTH domain-containing family protein 1 / DF1 / Dermatomyositis associated with cancer putative autoantigen 1 / DACA-1


Mass: 23148.166 Da / Num. of mol.: 12 / Fragment: YTH domain (residues 361-559)
Mutation: First residue G derives from the expression tag: E544A/E545V/E546V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDF1, C20orf21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BYJ9
#2: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.38 Å3/Da / Density % sol: 48.42 % / Mosaicity: 0.09 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 6-12% PEG3350, 0.2 M KSCN

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9429 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9429 Å / Relative weight: 1
ReflectionResolution: 2.5→49.05 Å / Num. obs: 87250 / % possible obs: 98.3 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.033 / Rrim(I) all: 0.061 / Net I/σ(I): 11.2 / Num. measured all: 301916
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
2.5-2.543.50.5771564644710.8120.360.6831.697.8
13.46-49.052.90.02215095150.9930.0160.02832.491.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.11.1refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RCI

4rci


Resolution: 2.5→48.095 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 28.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2427 4291 4.92 %
Rwork0.1843 82912 -
obs0.1872 87203 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.46 Å2 / Biso mean: 62.7219 Å2 / Biso min: 24.61 Å2
Refinement stepCycle: final / Resolution: 2.5→48.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18362 0 36 303 18701
Biso mean--87.57 50.82 -
Num. residues----2229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118940
X-RAY DIFFRACTIONf_angle_d1.17325479
X-RAY DIFFRACTIONf_chiral_restr0.0642643
X-RAY DIFFRACTIONf_plane_restr0.0093256
X-RAY DIFFRACTIONf_dihedral_angle_d17.07111446
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A10932X-RAY DIFFRACTION13.727TORSIONAL
12B10932X-RAY DIFFRACTION13.727TORSIONAL
13C10932X-RAY DIFFRACTION13.727TORSIONAL
14D10932X-RAY DIFFRACTION13.727TORSIONAL
15E10932X-RAY DIFFRACTION13.727TORSIONAL
16F10932X-RAY DIFFRACTION13.727TORSIONAL
17G10932X-RAY DIFFRACTION13.727TORSIONAL
18H10932X-RAY DIFFRACTION13.727TORSIONAL
19I10932X-RAY DIFFRACTION13.727TORSIONAL
110J10932X-RAY DIFFRACTION13.727TORSIONAL
111K10932X-RAY DIFFRACTION13.727TORSIONAL
112L10932X-RAY DIFFRACTION13.727TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.52840.38071530.2935275598
2.5284-2.55820.35321430.2766275698
2.5582-2.58930.33251740.2722269697
2.5893-2.62210.33141320.2686274698
2.6221-2.65660.35511420.2596275798
2.6566-2.6930.33261580.2562273198
2.693-2.73150.31091530.2408280198
2.7315-2.77220.29261470.2306271698
2.7722-2.81560.28741190.2329279098
2.8156-2.86170.30661460.2359274898
2.8617-2.91110.31121380.2451280198
2.9111-2.9640.34831370.2562277198
2.964-3.0210.30041360.2444275298
3.021-3.08260.31131490.2211278798
3.0826-3.14970.27981420.2176271798
3.1497-3.22290.30011490.2152281899
3.2229-3.30350.28671370.2094275898
3.3035-3.39280.25881270.2003276398
3.3928-3.49260.23131520.2004274199
3.4926-3.60530.26451310.1952278899
3.6053-3.73410.27071310.1842283299
3.7341-3.88350.25711460.1826275399
3.8835-4.06020.25361450.1634278599
4.0602-4.27410.19721400.1494276899
4.2741-4.54170.18171500.1377278599
4.5417-4.89210.17341490.1269272998
4.8921-5.38380.20561540.1364277199
5.3838-6.16150.18451420.1581279499
6.1615-7.75760.21711300.1735279599
7.7576-48.0950.18751390.1596270896
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)
14.29740.8341.8045.73341.69275.92190.0342-0.913-0.22780.6388-0.8022-0.3771.04340.09190.67340.6176-0.09980.07090.53710.18070.478524.49780.477367.2293
21.8059-0.83810.60050.91650.41322.22170.1394-0.28250.00460.2511-0.10720.18780.5284-0.0457-0.09750.5052-0.07940.04480.336-0.0030.409915.653-7.067649.6288
31.473-0.37890.8091.93470.21212.70870.00480.18730.1875-0.0588-0.1441-0.03450.0985-0.0390.0950.27610.00210.09060.310.02610.35717.31392.192646.5828
43.20051.01960.45830.7299-0.33790.64240.1224-0.20381.5191-0.0136-0.4764-0.8888-0.77010.96420.47240.7694-0.20080.04330.5947-0.00230.870618.944913.777347.5432
51.3478-0.56710.51991.0529-0.19841.799-0.12470.2629-0.2499-0.0394-0.0381-0.02220.66470.27910.07610.58070.02940.07850.3134-0.03570.472622.0042-11.195242.1113
65.8275-0.49352.22827.5033.14994.9491-0.1544-0.07750.0037-0.5129-0.18590.57390.49150.32840.08970.40290.00920.05580.38210.01490.420418.0473-4.150136.628
73.855-0.37660.97972.75630.19943.2887-0.1767-0.2882-0.44570.2255-0.0698-0.06820.9262-0.21270.20860.7844-0.04240.1510.29810.04640.502819.0237-15.108448.8607
81.04320.9184-0.12693.6988-0.3991.8809-0.15740.10750.06110.040.2862-0.03340.07040.038-0.1730.29680.046-0.00230.39650.0550.380635.774413.043156.1526
91.8795-0.0595-0.85594.37631.08132.474-0.0436-0.0234-0.1771-0.07350.0926-0.1213-0.06770.0749-0.06520.2564-0.0358-0.06850.35610.04360.3836.88830.228568.9165
100.6981-0.22370.21012.48570.33251.2467-0.0335-0.2154-0.10.61070.0628-0.40530.14670.18130.00440.35110.0003-0.07240.39880.06280.39436.116325.963876.9949
113.10110.44191.99944.8013-0.36143.42440.1405-0.8233-0.35740.9855-0.4158-0.4080.0708-0.07930.03420.43030.07450.06360.56130.11190.684456.255614.363544.2239
121.3431-0.78051.21542.02040.31013.0114-0.1109-0.0510.1639-0.3874-0.1414-0.44910.0480.24570.24810.33690.05610.10570.43790.10820.463641.570622.207730.603
132.45230.39840.84010.8115-0.14611.1350.0127-0.009-0.70090.26640.2807-0.3193-0.0275-0.1939-0.26620.43970.08680.08940.41150.07450.561541.22099.335438.6866
141.4043-1.00820.09852.29130.68383.0490.11390.2088-0.1271-0.3449-0.17020.177-0.2046-0.32350.06830.30420.02290.06140.5194-0.02810.488536.277115.508628.1733
152.4383-0.59230.31360.55761.05662.2749-0.1676-0.0123-0.2762-0.0139-0.12080.11970.0983-0.10670.23620.27760.01310.0680.48450.08940.509134.810619.982133.0841
162.2874-0.7723-0.58261.93771.13830.6751-0.0561-0.1270.176-0.6772-0.01631.24660.3184-0.63720.19560.31830.0180.01440.70340.03590.390728.390119.493829.3585
171.80230.12840.78291.5055-0.11332.96270.23740.3256-0.081-0.26890.0918-0.2936-0.34750.7216-0.06040.32560.02860.04740.50730.07730.509540.06830.176534.1228
181.87830.9903-0.59043.9061-0.99131.3515-0.1812-0.1442-0.51090.0110.1062-0.29340.54640.31920.01740.50130.1695-0.03120.49980.12750.6542.22281.744450.7038
192.28551.14610.57253.4383-0.16253.3592-0.3936-0.6579-0.22670.9396-0.19290.99760.545-0.80710.45770.7057-0.15440.25350.5893-0.1890.6581-0.295915.69679.9737
201.81340.38-0.65643.05420.62143.0144-0.027-0.32350.34280.2354-0.31940.0632-0.0327-0.14360.34880.3342-0.0785-0.00560.3418-0.01540.412110.329928.05479.5717
211.3069-0.6104-0.97562.82090.6763.4536-0.0444-0.01470.00470.0252-0.43150.3147-0.0891-0.17770.44440.2891-0.0818-0.0190.3774-0.05790.51535.228628.149472.2248
223.11780.64860.60881.09870.11681.50380.2774-0.00450.1660.5396-0.256-0.17440.78130.45610.04070.73990.0424-0.00570.48730.13430.562626.687512.006380.8477
231.5936-0.37311.05690.94740.19382.73020.25210.2143-0.6207-0.26340.48410.33950.475-1.5563-0.61080.6867-0.30380.00311.02360.03680.8172-12.5259-6.78820.884
241.8838-0.79061.67911.85570.0521.88830.05820.13580.1311-0.04660.1850.2194-0.3176-0.21430.31640.3402-0.04810.02010.44080.00590.422.75263.928423.3366
252.21550.5261.87090.30930.51281.8813-0.24070.0232-0.389-0.34670.25380.0124-0.1936-0.6637-0.0170.4045-0.0869-0.00860.8235-0.01910.49770.893-1.364713.0188
262.9405-1.42010.21942.11920.50032.22920.0718-0.0165-0.0042-0.06030.0383-0.16830.1947-0.1241-0.05510.2801-0.08380.02250.3617-0.03980.50642.7168-1.573425.9808
272.5556-1.410.17912.5956-0.54612.18930.25380.33060.0773-0.6038-0.0788-0.16550.2151-0.1866-0.22190.4252-0.06850.05820.5175-0.03950.52050.3146-2.129319.108
281.51280.59760.87021.42840.3761.530.0492-0.0003-0.01620.142-0.08340.1116-0.1429-0.47260.03280.26970.02810.04080.5871-0.01130.5264-5.25458.148930.9073
293.58340.5099-1.9841.41460.04132.84110.14130.67470.0016-0.45660.1969-0.0233-0.1518-0.7171-0.06440.6331-0.1353-0.07310.740.04360.47012.03841.8017-0.5958
300.6371-0.0532-0.02170.1499-0.14430.1269-0.12590.86640.5925-0.587-0.1622-0.682-0.40390.62060.05680.8445-0.20310.30540.8169-0.04930.987519.57571.116893.2051
310.7997-0.1419-0.19161.5736-0.37072.6911-0.0655-0.05540.40290.10840.0239-0.50110.11880.53180.10280.5197-0.0346-0.00630.5877-0.07890.523916.3313-10.5636110.5979
321.88080.3817-0.66570.5544-1.00861.8392-0.4357-0.09780.0394-0.2420.0431-0.4055-0.60670.24650.17250.6506-0.19120.04160.48080.00930.41397.88940.5453104.815
331.9492-0.21150.06263.09741.10333.3870.2034-0.38750.0530.09310.264-0.4326-0.47670.2421-0.45520.5388-0.15470.05240.5306-0.06450.479710.5666-6.1458115.6643
340.8472-0.21160.16762.6801-0.09742.9784-0.33360.07780.2476-0.14020.14110.7517-0.918-0.32280.06341.0668-0.01920.04120.5102-0.1650.66928.57775.2104114.4279
350.56670.61270.22811.5878-0.29912.1219-0.09750.0764-0.0678-0.07290.2047-0.16650.24070.1474-0.09950.4925-0.06620.04650.43-0.04090.355510.7349-17.5665110.1416
362.8467-1.82070.27484.06140.43870.61370.17340.08260.4185-0.4752-0.0835-0.2859-0.3484-0.08470.06670.9078-0.13320.1920.52570.02640.4581.1057.207694.352
371.8187-0.2611-0.96843.86340.29064.4684-0.0619-0.227-0.07170.13310.20880.1815-0.13530.1916-0.18850.42010.1480.03640.3937-0.02110.3925.0518-29.601731.1697
381.5935-0.7879-0.18641.86680.14212.4287-0.3424-0.4064-0.24760.43080.1815-0.3187-0.02680.13990.05860.45660.10880.0350.38430.00480.449827.3443-32.065432.1302
394.28120.5535-0.96563.52971.58712.583-0.4526-0.1129-0.0254-0.1212-0.08770.62881.26390.28210.50010.74030.0329-0.05590.4159-0.01880.651625.4724-45.648818.6566
401.6974-0.2775-0.37152.07870.09433.1077-0.21550.1669-0.51730.00230.01020.15090.4378-0.19290.24660.43640.0653-0.02970.4462-0.04150.593619.8878-39.620825.9856
413.52070.07340.8251.63810.36680.7315-0.08-0.8830.57350.64090.3824-0.07820.22570.6048-0.39310.94220.3964-0.11441.195-0.16030.562939.088-32.354249.2595
420.42570.7267-0.29571.2556-0.56261.00130.3959-0.15070.5366-0.07150.30880.1251-0.3146-0.13030.35861.8969-0.49970.8604-0.0802-0.02391.12061.0999-4.403180.7035
430.0295-0.04140.02213.11391.31710.55120.77130.11750.3187-0.5864-0.2435-1.6514-1.03340.57270.24631.5733-0.20880.52180.61520.16010.696410.2862-19.089668.5233
442.73570.0157-0.45963.26131.98353.55130.3932-0.1367-0.0593-0.4297-0.22680.0013-0.842-0.1616-0.15450.7611-0.08740.0130.36540.04010.3394-3.6025-25.481377.9034
453.0715-0.8184-0.53831.2716-0.81011.34830.86860.7736-0.1308-1.3757-0.6184-0.1487-1.778-0.44940.08811.53990.14830.18320.57420.05450.3018-1.7573-24.142563.0476
462.6882-0.1088-1.26470.3722-0.63182.44380.2519-0.06370.065-0.9079-0.2999-0.0151-0.488-0.22010.37361.40970.02630.12370.4258-0.10820.494-17.87-9.572586.311
471.4533-0.64440.86361.28790.37861.4482-0.13810.19150.0675-0.3250.02180.0175-0.41380.03190.08390.6166-0.1040.09050.55290.0430.448520.446419.38460.0526
481.1077-0.05661.36321.5283-0.9762.2670.14290.19970.0483-0.3116-0.3981-0.1902-0.11850.13020.16310.4621-0.0832-0.0470.6451-0.00440.492210.165317.11466.5449
492.9434-0.66010.00351.95650.83513.7089-0.3297-0.17-0.15190.1970.0836-0.1201-0.22160.0210.180.5156-0.01020.01840.39340.03730.408323.344819.706514.9252
500.97110.280.70511.84110.2971.3083-0.2992-0.2977-0.27710.23710.08390.19740.4738-0.47370.12280.4913-0.03420.04930.40370.02890.464415.325117.934710.4756
511.55180.30260.38611.68450.08541.7972-0.16620.2676-0.277-0.4780.1274-0.36210.27980.3645-0.01360.6094-0.08180.16290.5473-0.05530.540427.31698.94023.6114
522.5456-0.1211-1.1011.4204-0.81151.45-0.34110.46370.0019-0.03160.22480.5409-0.3624-0.3875-0.02490.6921-0.0429-0.15390.9724-0.04270.8981-3.444813.99453.6833
531.45140.2285-0.72992.09150.01633.3950.1482-0.17160.1797-0.3231-0.09410.1102-0.3526-0.0781-0.0260.72640.0360.02640.4202-0.05340.3803-19.18734.7794108.2845
542.3023-1.2236-0.55521.61510.69211.7890.0757-0.1063-0.0968-0.57080.05-0.1836-0.1276-0.0006-0.07610.9312-0.1280.11550.4155-0.00720.4657-2.9331-5.82691.3141
557.48560.3047-2.85842.3071-2.39183.9341-0.0479-0.0129-0.45930.31270.43910.53240.23510.35870.02890.75950.3917-0.08441.3261-0.08730.57719.894536.04850.18
561.53351.1767-0.36211.7223-0.65081.7317-0.27480.1845-0.6512-0.05030.458-1.21450.27570.4128-0.27180.57130.1799-0.09981.073-0.27420.811433.011745.39336.8619
572.10680.5327-0.89733.5992-0.05823.461-0.54330.39290.23010.17680.32550.1664-1.0475-0.74030.1880.54490.1855-0.13210.8131-0.05240.506117.393850.564230.0952
580.5413-0.2606-0.11751.0128-0.17491.8367-0.0943-0.67890.06250.64720.34520.3127-0.1610.1653-0.16970.68780.32310.00960.94870.03660.423512.370542.377637.7618
592.31520.5193-0.71983.46150.953.5279-0.2647-0.27020.3019-0.48920.5273-0.1151-0.07680.1516-0.21640.48570.1396-0.04690.4917-0.01160.311220.498644.473624.3057
600.3308-0.1004-0.47311.3120.02421.3857-0.5485-0.44740.0623-0.18030.25150.5933-0.0933-0.11170.30550.48610.2433-0.0520.7814-0.01630.612814.773243.361132.0939
610.96330.1468-0.01492.3170.13252.6381-0.2146-0.7440.455-0.02390.4836-0.2569-0.30270.4915-0.19730.51650.1866-0.12340.8832-0.22840.600824.727456.658833.9293
624.58151.01120.83781.4994-0.04121.1723-0.0201-0.30690.22850.42690.11670.21890.55160.3946-0.09080.80540.37540.04991.0190.01570.54661.517440.451446.4595
631.04450.0682-0.01492.1706-0.28421.79790.27330.19150.1753-0.1238-0.46780.9258-0.7548-0.49990.21270.94850.1729-0.19540.5923-0.23350.821235.9979-23.917381.2499
643.10621.94210.65673.3952-2.5184.44210.63570.6592-1.1688-1.0702-1.33070.4799-0.2219-0.4769-0.00960.60230.2202-0.44840.6879-0.41980.860542.3613-38.642273.9437
651.61341.056-0.45672.0258-0.10242.08380.55730.2267-0.3189-0.009-0.50620.8173-0.3761-0.23730.03460.73230.0949-0.29960.5141-0.23920.774738.4914-29.786583.8553
662.0089-0.19580.57513.8710.35572.30860.2997-0.04410.01550.0915-0.5790.6743-0.2354-0.21860.17690.67320.0017-0.09530.5625-0.21320.644940.1411-30.733488.2431
670.6735-0.54930.18650.5929-0.25140.9191-0.17850.70790.2774-0.6966-0.06830.03470.2004-0.18350.29271.58360.146-0.15880.6313-0.00380.714549.4626-9.07572.7155
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 365 through 374 )A365 - 374
2X-RAY DIFFRACTION2chain 'A' and (resid 375 through 398 )A375 - 398
3X-RAY DIFFRACTION3chain 'A' and (resid 399 through 457 )A399 - 457
4X-RAY DIFFRACTION4chain 'A' and (resid 458 through 475 )A458 - 475
5X-RAY DIFFRACTION5chain 'A' and (resid 476 through 504 )A476 - 504
6X-RAY DIFFRACTION6chain 'A' and (resid 505 through 512 )A505 - 512
7X-RAY DIFFRACTION7chain 'A' and (resid 513 through 531 )A513 - 531
8X-RAY DIFFRACTION8chain 'A' and (resid 532 through 559 )A532 - 559
9X-RAY DIFFRACTION9chain 'B' and (resid 365 through 475 )B365 - 475
10X-RAY DIFFRACTION10chain 'B' and (resid 476 through 559 )B476 - 559
11X-RAY DIFFRACTION11chain 'C' and (resid 364 through 374 )C364 - 374
12X-RAY DIFFRACTION12chain 'C' and (resid 375 through 398 )C375 - 398
13X-RAY DIFFRACTION13chain 'C' and (resid 399 through 414 )C399 - 414
14X-RAY DIFFRACTION14chain 'C' and (resid 415 through 452 )C415 - 452
15X-RAY DIFFRACTION15chain 'C' and (resid 453 through 504 )C453 - 504
16X-RAY DIFFRACTION16chain 'C' and (resid 505 through 512 )C505 - 512
17X-RAY DIFFRACTION17chain 'C' and (resid 513 through 531 )C513 - 531
18X-RAY DIFFRACTION18chain 'C' and (resid 532 through 558 )C532 - 558
19X-RAY DIFFRACTION19chain 'D' and (resid 364 through 388 )D364 - 388
20X-RAY DIFFRACTION20chain 'D' and (resid 389 through 452 )D389 - 452
21X-RAY DIFFRACTION21chain 'D' and (resid 453 through 531 )D453 - 531
22X-RAY DIFFRACTION22chain 'D' and (resid 532 through 558 )D532 - 558
23X-RAY DIFFRACTION23chain 'E' and (resid 365 through 388 )E365 - 388
24X-RAY DIFFRACTION24chain 'E' and (resid 389 through 398 )E389 - 398
25X-RAY DIFFRACTION25chain 'E' and (resid 399 through 414 )E399 - 414
26X-RAY DIFFRACTION26chain 'E' and (resid 415 through 452 )E415 - 452
27X-RAY DIFFRACTION27chain 'E' and (resid 453 through 488 )E453 - 488
28X-RAY DIFFRACTION28chain 'E' and (resid 489 through 531 )E489 - 531
29X-RAY DIFFRACTION29chain 'E' and (resid 532 through 558 )E532 - 558
30X-RAY DIFFRACTION30chain 'F' and (resid 364 through 374 )F364 - 374
31X-RAY DIFFRACTION31chain 'F' and (resid 375 through 398 )F375 - 398
32X-RAY DIFFRACTION32chain 'F' and (resid 399 through 414 )F399 - 414
33X-RAY DIFFRACTION33chain 'F' and (resid 415 through 452 )F415 - 452
34X-RAY DIFFRACTION34chain 'F' and (resid 453 through 475 )F453 - 475
35X-RAY DIFFRACTION35chain 'F' and (resid 476 through 531 )F476 - 531
36X-RAY DIFFRACTION36chain 'F' and (resid 532 through 558 )F532 - 558
37X-RAY DIFFRACTION37chain 'G' and (resid 365 through 440 )G365 - 440
38X-RAY DIFFRACTION38chain 'G' and (resid 441 through 488 )G441 - 488
39X-RAY DIFFRACTION39chain 'G' and (resid 489 through 504 )G489 - 504
40X-RAY DIFFRACTION40chain 'G' and (resid 505 through 531 )G505 - 531
41X-RAY DIFFRACTION41chain 'G' and (resid 532 through 557 )G532 - 557
42X-RAY DIFFRACTION42chain 'H' and (resid 365 through 374 )H365 - 374
43X-RAY DIFFRACTION43chain 'H' and (resid 375 through 388 )H375 - 388
44X-RAY DIFFRACTION44chain 'H' and (resid 389 through 475 )H389 - 475
45X-RAY DIFFRACTION45chain 'H' and (resid 476 through 531 )H476 - 531
46X-RAY DIFFRACTION46chain 'H' and (resid 532 through 559 )H532 - 559
47X-RAY DIFFRACTION47chain 'I' and (resid 364 through 398 )I364 - 398
48X-RAY DIFFRACTION48chain 'I' and (resid 399 through 414 )I399 - 414
49X-RAY DIFFRACTION49chain 'I' and (resid 415 through 440 )I415 - 440
50X-RAY DIFFRACTION50chain 'I' and (resid 441 through 475 )I441 - 475
51X-RAY DIFFRACTION51chain 'I' and (resid 476 through 531 )I476 - 531
52X-RAY DIFFRACTION52chain 'I' and (resid 532 through 558 )I532 - 558
53X-RAY DIFFRACTION53chain 'J' and (resid 365 through 531 )J365 - 531
54X-RAY DIFFRACTION54chain 'J' and (resid 532 through 559 )J532 - 559
55X-RAY DIFFRACTION55chain 'K' and (resid 365 through 374 )K365 - 374
56X-RAY DIFFRACTION56chain 'K' and (resid 375 through 388 )K375 - 388
57X-RAY DIFFRACTION57chain 'K' and (resid 389 through 398 )K389 - 398
58X-RAY DIFFRACTION58chain 'K' and (resid 399 through 414 )K399 - 414
59X-RAY DIFFRACTION59chain 'K' and (resid 415 through 440 )K415 - 440
60X-RAY DIFFRACTION60chain 'K' and (resid 441 through 475 )K441 - 475
61X-RAY DIFFRACTION61chain 'K' and (resid 476 through 531 )K476 - 531
62X-RAY DIFFRACTION62chain 'K' and (resid 532 through 558 )K532 - 558
63X-RAY DIFFRACTION63chain 'L' and (resid 366 through 414 )L366 - 414
64X-RAY DIFFRACTION64chain 'L' and (resid 415 through 428 )L415 - 428
65X-RAY DIFFRACTION65chain 'L' and (resid 429 through 452 )L429 - 452
66X-RAY DIFFRACTION66chain 'L' and (resid 453 through 531 )L453 - 531
67X-RAY DIFFRACTION67chain 'L' and (resid 532 through 558 )L532 - 558

+
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