[English] 日本語
Yorodumi
- PDB-5els: Structure of the KH domain of T-STAR in complex with AAAUAA RNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5els
TitleStructure of the KH domain of T-STAR in complex with AAAUAA RNA
Components
  • KH domain-containing, RNA-binding, signal transduction-associated protein 3
  • RNA (5'-R(P*AP*AP*AP*UP*AP*A)-3')
KeywordsRNA BINDING PROTEIN / Protein - RNA complexes STAR protein Alternative splicing KH domain
Function / homology
Function and homology information


PTK6 Regulates Proteins Involved in RNA Processing / regulation of alternative mRNA splicing, via spliceosome / mRNA processing / SH3 domain binding / protein domain specific binding / mRNA binding / protein-containing complex / RNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Sam68, tyrosine-rich domain / KHDRBS, Qua1 domain / Qua1 domain / Tyrosine-rich domain of Sam68 / KH domain-containing BBP-like / KH domain / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain
Similarity search - Domain/homology
RNA / KH domain-containing, RNA-binding, signal transduction-associated protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.873 Å
AuthorsDominguez, C. / Feracci, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1000526 United Kingdom
CitationJournal: Nat Commun / Year: 2016
Title: Structural basis of RNA recognition and dimerization by the STAR proteins T-STAR and Sam68.
Authors: Feracci, M. / Foot, J.N. / Grellscheid, S.N. / Danilenko, M. / Stehle, R. / Gonchar, O. / Kang, H.S. / Dalgliesh, C. / Meyer, N.H. / Liu, Y. / Lahat, A. / Sattler, M. / Eperon, I.C. / ...Authors: Feracci, M. / Foot, J.N. / Grellscheid, S.N. / Danilenko, M. / Stehle, R. / Gonchar, O. / Kang, H.S. / Dalgliesh, C. / Meyer, N.H. / Liu, Y. / Lahat, A. / Sattler, M. / Eperon, I.C. / Elliott, D.J. / Dominguez, C.
History
DepositionNov 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Data collection / Category: diffrn_radiation_wavelength / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: KH domain-containing, RNA-binding, signal transduction-associated protein 3
B: KH domain-containing, RNA-binding, signal transduction-associated protein 3
C: KH domain-containing, RNA-binding, signal transduction-associated protein 3
D: KH domain-containing, RNA-binding, signal transduction-associated protein 3
E: KH domain-containing, RNA-binding, signal transduction-associated protein 3
F: KH domain-containing, RNA-binding, signal transduction-associated protein 3
H: RNA (5'-R(P*AP*AP*AP*UP*AP*A)-3')
I: RNA (5'-R(P*AP*AP*AP*UP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,19111
Polymers80,9038
Non-polymers2883
Water00
1
A: KH domain-containing, RNA-binding, signal transduction-associated protein 3
C: KH domain-containing, RNA-binding, signal transduction-associated protein 3
H: RNA (5'-R(P*AP*AP*AP*UP*AP*A)-3')
I: RNA (5'-R(P*AP*AP*AP*UP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6075
Polymers29,5114
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: KH domain-containing, RNA-binding, signal transduction-associated protein 3
F: KH domain-containing, RNA-binding, signal transduction-associated protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8884
Polymers25,6962
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: KH domain-containing, RNA-binding, signal transduction-associated protein 3
E: KH domain-containing, RNA-binding, signal transduction-associated protein 3


Theoretical massNumber of molelcules
Total (without water)25,6962
Polymers25,6962
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.730, 162.220, 113.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 48:51 or resseq 53:58 or resseq...
21(chain B and (resseq 48:51 or resseq 53:58 or resseq...
31(chain C and (resseq 48:51 or resseq 53:58 or resseq...
41(chain D and (resseq 48:51 or resseq 53:58 or resseq...
51(chain E and (resseq 48:51 or resseq 53:58 or resseq...
61(chain F and (resseq 48:51 or resseq 53:58 or resseq...

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
11GLYGLYASNASN(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA48 - 511 - 4
12ASNASNGLNGLN(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA53 - 586 - 11
13VALVALVALVAL(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA60 - 6413 - 17
14PHEPHEPROPRO(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA67 - 6820 - 21
15PHEPHEGLYGLY(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA70 - 7423 - 27
16LEULEUPROPRO(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA76 - 7929 - 32
17GLYGLYLEULEU(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA81 - 8434 - 37
18LEULEUGLNGLN(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA87 - 8840 - 41
19THRTHRLYSLYS(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA91 - 9444 - 47
110SERSERGLYGLY(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA96 - 9949 - 52
111GLYGLYMETMET(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA101 - 10354 - 56
112ASPASPASPASP(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA10558
113ALAALAALAALA(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA10760
114GLUGLUGLUGLU(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA109 - 11062 - 63
115LEULEUARGARG(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA112 - 11365 - 66
116SERSERGLYGLY(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA115 - 11668 - 69
117ALAALAALAALA(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA118 - 14271 - 95
118METMETLEULEU(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA144 - 14897 - 101
119GLUGLULYSLYS(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA150 - 152103 - 105
120PHEPHEPROPRO(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA154 - 157107 - 110
21GLYGLYASNASN(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB48 - 511 - 4
22ASNASNGLNGLN(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB53 - 586 - 11
23VALVALVALVAL(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB60 - 6413 - 17
24PHEPHEPROPRO(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB67 - 6820 - 21
25PHEPHEGLYGLY(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB70 - 7423 - 27
26LEULEUPROPRO(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB76 - 7929 - 32
27GLYGLYLEULEU(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB81 - 8434 - 37
28LEULEUGLNGLN(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB87 - 8840 - 41
29THRTHRLYSLYS(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB91 - 9444 - 47
210SERSERGLYGLY(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB96 - 9949 - 52
211GLYGLYMETMET(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB101 - 10354 - 56
212ASPASPASPASP(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB10558
213ALAALAALAALA(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB10760
214GLUGLUGLUGLU(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB109 - 11062 - 63
215LEULEUARGARG(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB112 - 11365 - 66
216SERSERGLYGLY(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB115 - 11668 - 69
217ALAALAALAALA(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB118 - 14271 - 95
218METMETLEULEU(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB144 - 14897 - 101
219GLUGLULYSLYS(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB150 - 152103 - 105
220PHEPHEPROPRO(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB154 - 157107 - 110
31GLYGLYASNASN(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC48 - 511 - 4
32ASNASNGLNGLN(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC53 - 586 - 11
33VALVALVALVAL(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC60 - 6413 - 17
34PHEPHEPROPRO(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC67 - 6820 - 21
35PHEPHEGLYGLY(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC70 - 7423 - 27
36LEULEUPROPRO(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC76 - 7929 - 32
37GLYGLYLEULEU(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC81 - 8434 - 37
38LEULEUGLNGLN(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC87 - 8840 - 41
39THRTHRLYSLYS(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC91 - 9444 - 47
310SERSERGLYGLY(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC96 - 9949 - 52
311GLYGLYMETMET(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC101 - 10354 - 56
312ASPASPASPASP(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC10558
313ALAALAALAALA(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC10760
314GLUGLUGLUGLU(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC109 - 11062 - 63
315LEULEUARGARG(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC112 - 11365 - 66
316SERSERGLYGLY(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC115 - 11668 - 69
317ALAALAALAALA(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC118 - 14271 - 95
318METMETLEULEU(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC144 - 14897 - 101
319GLUGLULYSLYS(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC150 - 152103 - 105
320PHEPHEPROPRO(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC154 - 157107 - 110
41GLYGLYASNASN(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD48 - 511 - 4
42ASNASNGLNGLN(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD53 - 586 - 11
43VALVALVALVAL(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD60 - 6413 - 17
44PHEPHEPROPRO(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD67 - 6820 - 21
45PHEPHEGLYGLY(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD70 - 7423 - 27
46LEULEUPROPRO(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD76 - 7929 - 32
47GLYGLYLEULEU(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD81 - 8434 - 37
48LEULEUGLNGLN(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD87 - 8840 - 41
49THRTHRLYSLYS(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD91 - 9444 - 47
410SERSERGLYGLY(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD96 - 9949 - 52
411GLYGLYMETMET(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD101 - 10354 - 56
412ASPASPASPASP(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD10558
413ALAALAALAALA(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD10760
414GLUGLUGLUGLU(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD109 - 11062 - 63
415LEULEUARGARG(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD112 - 11365 - 66
416SERSERGLYGLY(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD115 - 11668 - 69
417ALAALAALAALA(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD118 - 14271 - 95
418METMETLEULEU(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD144 - 14897 - 101
419GLUGLULYSLYS(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD150 - 152103 - 105
420PHEPHEPROPRO(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD154 - 157107 - 110
51GLYGLYASNASN(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE48 - 511 - 4
52ASNASNGLNGLN(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE53 - 586 - 11
53VALVALVALVAL(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE60 - 6413 - 17
54PHEPHEPROPRO(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE67 - 6820 - 21
55PHEPHEGLYGLY(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE70 - 7423 - 27
56LEULEUPROPRO(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE76 - 7929 - 32
57GLYGLYLEULEU(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE81 - 8434 - 37
58LEULEUGLNGLN(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE87 - 8840 - 41
59THRTHRLYSLYS(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE91 - 9444 - 47
510SERSERGLYGLY(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE96 - 9949 - 52
511GLYGLYMETMET(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE101 - 10354 - 56
512ASPASPASPASP(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE10558
513ALAALAALAALA(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE10760
514GLUGLUGLUGLU(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE109 - 11062 - 63
515LEULEUARGARG(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE112 - 11365 - 66
516SERSERGLYGLY(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE115 - 11668 - 69
517ALAALAALAALA(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE118 - 14271 - 95
518METMETLEULEU(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE144 - 14897 - 101
519GLUGLULYSLYS(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE150 - 152103 - 105
520PHEPHEPROPRO(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE154 - 157107 - 110
61GLYGLYASNASN(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF48 - 511 - 4
62ASNASNGLNGLN(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF53 - 586 - 11
63VALVALVALVAL(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF60 - 6413 - 17
64PHEPHEPROPRO(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF67 - 6820 - 21
65PHEPHEGLYGLY(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF70 - 7423 - 27
66LEULEUPROPRO(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF76 - 7929 - 32
67GLYGLYLEULEU(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF81 - 8434 - 37
68LEULEUGLNGLN(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF87 - 8840 - 41
69THRTHRLYSLYS(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF91 - 9444 - 47
610SERSERGLYGLY(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF96 - 9949 - 52
611GLYGLYMETMET(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF101 - 10354 - 56
612ASPASPASPASP(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF10558
613ALAALAALAALA(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF10760
614GLUGLUGLUGLU(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF109 - 11062 - 63
615LEULEUARGARG(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF112 - 11365 - 66
616SERSERGLYGLY(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF115 - 11668 - 69
617ALAALAALAALA(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF118 - 14271 - 95
618METMETLEULEU(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF144 - 14897 - 101
619GLUGLULYSLYS(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF150 - 152103 - 105
620PHEPHEPROPRO(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF154 - 157107 - 110

-
Components

#1: Protein
KH domain-containing, RNA-binding, signal transduction-associated protein 3 / RNA-binding protein T-Star / Sam68-like mammalian protein 2 / SLM-2 / Sam68-like phosphotyrosine protein


Mass: 12848.066 Da / Num. of mol.: 6 / Fragment: RNA binding protein, UNP residues 50-160
Source method: isolated from a genetically manipulated source
Details: N-terminus GA residues from tag. / Source: (gene. exp.) Homo sapiens (human) / Gene: KHDRBS3, SALP, SLM2 / Plasmid: pLEICS 03 / Production host: Escherichia coli (E. coli) / References: UniProt: O75525
#2: RNA chain RNA (5'-R(P*AP*AP*AP*UP*AP*A)-3')


Mass: 1907.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Lithium sulphate, Tris

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
Reflection twinOperator: 1/2*h+1/2*k,3/2*h-1/2*k,-l / Fraction: 0.25
ReflectionResolution: 2.873→46.865 Å / Num. all: 20014 / Num. obs: 20014 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rpim(I) all: 0.078 / Rrim(I) all: 0.206 / Rsym value: 0.174 / Net I/av σ(I): 3.5 / Net I/σ(I): 8.1 / Num. measured all: 137466
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.87-2.957.20.74511069014750.3210.7452.4100
2.95-3.037.20.5991.31030914350.2580.5993.199.8
3.03-3.127.10.511.5976613680.2220.513.699.8
3.12-3.217.20.4261.8965513440.1860.4264.299.9
3.21-3.326.90.3582.1892713000.1590.3584.7100
3.32-3.436.60.2832.7830112510.130.2835.899.6
3.43-3.5660.2333.3738612230.1150.2336.499.6
3.56-3.7160.1864704011740.0930.1867.899.8
3.71-3.877.30.1784.2841111500.0780.1789.5100
3.87-4.067.20.1534.8782110860.0670.15310.899.8
4.06-4.287.20.1394.8737010290.0640.13911.499.9
4.28-4.547.10.1315.567839550.0580.13111.8100
4.54-4.867.10.1235.765859280.0550.12312.399.9
4.86-5.256.90.1345.460878830.060.13411.299.9
5.25-5.756.70.1245.851617730.0580.12411.1100
5.75-6.426.50.1225.647347310.0570.12211.399.6
6.42-7.425.50.1016.535656440.0530.10111.899.5
7.42-9.087.30.0827.740795580.0350.08215.9100
9.08-12.857.10.0689.431154410.0280.06817100
12.85-46.8656.30.0628.316812660.0280.0621798.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.20data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.873→46.865 Å / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.47 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 1021 5.11 %RAMDOM
Rwork0.1875 18918 --
obs0.1897 19995 99.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 198.12 Å2 / Biso mean: 52.3359 Å2 / Biso min: 11.2 Å2
Refinement stepCycle: final / Resolution: 2.873→46.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5356 260 15 0 5631
Biso mean--58.75 --
Num. residues----684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135760
X-RAY DIFFRACTIONf_angle_d1.4617756
X-RAY DIFFRACTIONf_chiral_restr0.076840
X-RAY DIFFRACTIONf_plane_restr0.012948
X-RAY DIFFRACTIONf_dihedral_angle_d18.2323538
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2116X-RAY DIFFRACTION13.758TORSIONAL
12B2116X-RAY DIFFRACTION13.758TORSIONAL
13C2116X-RAY DIFFRACTION13.758TORSIONAL
14D2116X-RAY DIFFRACTION13.758TORSIONAL
15E2116X-RAY DIFFRACTION13.758TORSIONAL
16F2116X-RAY DIFFRACTION13.758TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8732-3.02440.32361440.25832690283495
3.0244-3.21330.27711440.23842652279695
3.2133-3.46060.2731410.22152666280795
3.4606-3.80740.24841640.18662643280794
3.8074-4.35490.21311440.1652711285595
4.3549-5.47360.21111420.1622729287195
5.4736-22.51260.1911410.16852827296895
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)
11.1565-0.47581.02620.5994-0.5750.83360.0463-0.13220.11230.1784-0.1148-0.11160.1628-0.22090.04840.22630.0023-0.07270.14380.02690.1793129.105934.1578126.0307
22.0880.47270.23181.7488-0.72782.70060.021-0.3979-0.4438-0.2422-0.1687-0.3575-0.28680.1522-0.03010.307-0.08910.00270.19790.0190.09123.866318.5951132.7831
31.3132-0.35140.30580.2572-0.05210.97930.13270.08750.1220.00240.00250.0545-0.19260.25670.08650.21360.02430.03750.14650.03150.1423130.231436.8637121.1921
40.1024-0.0905-0.02730.10520.0410.01590.1578-0.37240.29190.36470.18750.2607-0.0099-0.34410.1040.74890.1260.07530.5230.02780.3935125.4462-14.0435171.8645
51.2905-0.62930.35582.14020.10630.14740.2629-0.3456-0.47010.29710.01790.0420.1206-0.2689-0.08830.3229-0.06090.00120.42450.15380.2466122.46220.2617163.7517
60.2757-0.10190.28710.3914-0.00780.3197-0.0481-0.0646-0.00680.1757-0.21910.0635-0.0022-0.2268-0.3626-0.1314-0.03970.55630.32120.1513-0.0781123.376920.78153.7128
70.94740.27761.4272.47571.07162.32310.22010.17580.0549-0.42510.0344-0.1297-0.13550.56020.28080.3019-0.19690.22610.1960.1482-0.1224128.625712.4385148.988
81.0288-0.039-0.12871.10590.74221.06930.040.016-0.238-0.0463-0.1929-0.03950.42780.0522-0.16490.55520.1520.07510.05950.13870.667133.92292.8888149.4528
92.3303-2.89891.4854.2643-1.05451.9305-0.243-0.1193-0.1046-0.1578-0.28910.08520.0747-0.1467-0.00280.3430.00880.11930.15690.09530.3463125.95881.3131154.8414
101.51710.5097-0.1770.7313-0.24270.894-0.1001-0.1612-0.0263-0.0963-0.07620.11470.0001-0.1301-0.17150.39160.2308-0.40230.65720.01340.671116.645112.1791146.8602
110.66610.32950.62633.33520.39950.9574-0.09640.3362-0.26610.0865-0.17050.43870.2554-0.23010.0110.8647-0.0111-0.22990.6058-0.02370.5051108.037910.2781145.7635
123.67981.3082-0.69461.6893-0.89880.51680.15410.1013-0.3263-0.18390.0820.40650.22210.0171-0.03460.33950.0073-0.07520.44740.20840.4293111.00196.2158153.2143
13-0.0044-0.0088-0.01620.00390.1321.62830.09630.1510.31240.1558-0.25890.03890.4483-0.136-0.04440.17570.0699-0.14390.23530.06060.36128.8457-0.5015163.3881
141.41820.00520.22592.9892-0.76121.3808-0.10670.15270.0656-0.0394-0.1219-0.30030.31650.20390.05040.1901-0.0177-0.06350.20840.06160.2875133.120716.8825154.4439
150.0584-0.04710.01230.05-0.05590.16770.0578-0.13740.03070.1257-0.06830.02870.02090.12-0.03220.6529-0.07320.27590.9616-0.42250.270298.476452.7048170.9656
160.8807-0.8566-0.94231.08220.64410.967-0.04910.1315-0.22040.0478-0.09270.1813-0.1676-0.14210.03870.1536-0.0066-0.01870.2211-0.030.1038117.303639.6959153.139
171.83170.6160.37712.2064-0.20441.605-0.31260.26890.079-0.5301-0.21650.0158-0.42070.1861-0.26750.1303-0.01420.06610.3213-0.08460.1325119.032746.1463149.8898
181.84010.452-0.65750.7081-0.45071.3832-0.04690.08640.1048-0.0190.0564-0.0435-0.01110.1250.03450.7384-0.0560.45010.65740.14570.4276129.448355.4967144.8376
190.7278-0.3548-0.50410.41950.36250.62880.03910.12570.1205-0.0705-0.05260.0867-0.03090.01610.00080.21450.00180.01830.18150.02790.1503116.044843.9336157.4025
200.5818-0.0545-0.85971.88760.8691.5406-0.1621-0.0560.13930.13690.1917-0.24720.3502-0.1633-0.03980.4888-0.04260.18970.3387-0.03420.2443116.043317.0323116.7381
214.1019-1.72870.70822.83790.40380.3580.037-0.2742-0.22960.17370.10270.5099-0.098-0.179-0.07010.5055-0.16390.41440.6343-0.16740.940591.278530.028119.0483
223.56412.2645-1.56762.69390.36022.14750.0861-0.0189-0.32480.4509-0.1094-0.22250.17410.47680.1590.8885-0.25760.36890.5185-0.01710.761494.855620.7063130.8688
230.1510.202-0.12232.3310.0940.2905-0.1088-0.04780.16780.32620.11990.36380.34380.0053-0.0310.5571-0.08290.10260.3884-0.00290.4256103.758415.9742127.0568
243.31090.8002-0.13682.0379-0.38611.8967-0.164-0.2450.11980.0568-0.39280.30440.1748-0.65350.13280.34880.13050.01590.5574-0.17730.3555104.742838.4829130.0839
250.38460.05720.14131.38090.46620.85510.1414-0.0558-0.1334-0.0206-0.19310.02550.1521-0.43720.05890.2726-0.11210.03910.2550.00640.308105.932820.8216120.0954
260.06740.39970.05712.42580.82664.4386-0.04240.1417-0.12-0.2869-0.05920.07980.1782-0.26630.18240.62970.07070.04841.0168-0.25470.2806100.500723.4833110.1664
274.7072-0.3196-0.12742.0910.18172.10080.06380.0086-0.07730.0060.1335-0.22610.1623-0.2915-0.02240.6327-0.09070.00710.24670.03250.2646116.099218.0705106.9287
280.6163-0.541-0.16943.00311.81641.1405-0.01710.2707-0.58160.05780.099-0.33020.6250.67540.07271.07680.17530.55570.7207-0.12110.8879134.63244.2589105.6245
292.1271-1.16374.13050.6611-2.21868.0662-0.08190.20030.1912-0.16140.2092-0.0718-0.04460.42790.02841.1594-0.06110.10740.55130.08370.9902127.06643.753597.6563
304.3893-2.1976-2.52732.70961.6671.66330.4390.4412-0.1355-0.6203-0.0086-0.0038-0.0115-0.0293-0.11030.7078-0.0305-0.02930.4625-0.04280.8174116.32464.484394.4902
310.30420.25070.01171.0039-0.13140.93230.01420.32860.014-0.5492-0.0742-0.2796-0.324-0.010.16170.6495-0.21080.24920.3768-0.17920.5728126.413313.693796.8936
320.568-0.0424-0.20330.4792-0.22540.2114-0.04560.06260.11590.0264-0.0776-0.0010.41990.3670.04350.4583-0.1020.1140.5275-0.12740.4532132.89223.414196.8411
331.40310.20980.29161.6452-0.5891.8328-0.01570.0212-0.53280.0301-0.2832-0.1650.12740.05060.09980.5372-0.15510.00840.2874-0.00480.386115.083510.1071106.2823
341.568-0.0315-0.53510.14350.28121.98080.50140.1114-0.10270.00110.34310.2418-0.1241-0.235-0.10260.34510.0893-0.06360.78760.1050.5867106.27863.1137165.345
350.1487-0.19640.79270.2503-1.02684.18620.0017-0.2648-0.20990.2461-0.10150.04770.1487-0.0572-0.07481.1275-0.1210.36420.98490.34960.7821105.5621-25.0522161.4699
362.11730.25710.18641.0892-0.41510.7047-0.06290.005-0.1589-0.1844-0.1029-0.17430.13150.04090.07740.6732-0.38140.39291.2624-0.10280.985899.3711-17.3209150.9423
370.16270.1990.01480.57040.26820.1837-0.0433-0.17220.11980.2127-0.02391.0527-0.2982-0.70240.16920.5489-0.09710.0491.13760.1410.894698.5541-7.1144154.5145
380.0729-0.09430.02190.85880.72960.7634-0.17050.1501-0.283-0.22940.1431-0.15280.6624-0.3140.02870.4742-0.092-0.00750.7376-0.0450.7173118.5502-15.4038153.0707
391.7440.8374-0.29140.7623-0.74641.8529-0.04270.6521-0.0823-0.24170.0236-0.13710.3636-0.75550.03080.1865-0.087-0.00481.06560.1960.605699.3705-7.1833163.0954
401.4479-0.2623-0.79310.6726-0.09080.51330.1198-0.1247-0.03050.5899-0.10310.2367-0.1441-0.191-0.02090.2916-0.0065-0.03360.4848-0.09420.2487125.011536.364140.2651
410.4539-0.0569-0.01551.21310.52080.23040.04180.37070.0594-0.02080.0078-0.10050.11920.0293-0.01410.51520.12130.00910.4020.07460.1645120.423738.8372141.4239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 48 through 98 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 99 through 127 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 128 through 160 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 48 through 52 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 53 through 61 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 62 through 71 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 72 through 78 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 79 through 91 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 92 through 98 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 99 through 105 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 106 through 115 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 116 through 127 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 128 through 150 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 151 through 160 )B0
15X-RAY DIFFRACTION15chain 'C' and (resid 48 through 52 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 53 through 91 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 92 through 105 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 106 through 114 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 115 through 160 )C0
20X-RAY DIFFRACTION20chain 'D' and (resid 48 through 61 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 62 through 72 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 73 through 82 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 83 through 98 )D0
24X-RAY DIFFRACTION24chain 'D' and (resid 99 through 117 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 118 through 158 )D0
26X-RAY DIFFRACTION26chain 'E' and (resid 48 through 52 )E0
27X-RAY DIFFRACTION27chain 'E' and (resid 53 through 61 )E0
28X-RAY DIFFRACTION28chain 'E' and (resid 62 through 71 )E0
29X-RAY DIFFRACTION29chain 'E' and (resid 72 through 78 )E0
30X-RAY DIFFRACTION30chain 'E' and (resid 79 through 91 )E0
31X-RAY DIFFRACTION31chain 'E' and (resid 92 through 106 )E0
32X-RAY DIFFRACTION32chain 'E' and (resid 107 through 127 )E0
33X-RAY DIFFRACTION33chain 'E' and (resid 128 through 157 )E0
34X-RAY DIFFRACTION34chain 'F' and (resid 48 through 61 )F0
35X-RAY DIFFRACTION35chain 'F' and (resid 62 through 71 )F0
36X-RAY DIFFRACTION36chain 'F' and (resid 72 through 81 )F0
37X-RAY DIFFRACTION37chain 'F' and (resid 82 through 98 )F0
38X-RAY DIFFRACTION38chain 'F' and (resid 99 through 127 )F0
39X-RAY DIFFRACTION39chain 'F' and (resid 128 through 159 )F0
40X-RAY DIFFRACTION40chain 'H' and (resid -1 through 4 )H0
41X-RAY DIFFRACTION41chain 'I' and (resid 0 through 5 )I0

+
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://pdbjlvh1.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