[English] 日本語
Yorodumi
- PDB-5nbn: Crystal structure of the Arp4-N-actin-Arp8-Ino80HSA module of INO80 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nbn
TitleCrystal structure of the Arp4-N-actin-Arp8-Ino80HSA module of INO80
Components
  • Actin-like protein ARP8
  • Actin-related protein 4
  • Actin
  • Putative DNA helicase INO80
KeywordsHYDROLASE / Chromatin remodeling / Nanobody / INO80 / SWR1 / NuA4
Function / homology
Function and homology information


mitotic actomyosin contractile ring contraction / RHOA GTPase cycle / cellular bud neck contractile ring / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / ascospore wall assembly / vacuole inheritance / actin cortical patch / Swr1 complex ...mitotic actomyosin contractile ring contraction / RHOA GTPase cycle / cellular bud neck contractile ring / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / ascospore wall assembly / vacuole inheritance / actin cortical patch / Swr1 complex / mitotic recombination / Platelet degranulation / regulation of TOR signaling / : / telomere maintenance via recombination / Ino80 complex / kinetochore assembly / regulation of metabolic process / SWI/SNF complex / ATP-dependent chromatin remodeler activity / NuA4 histone acetyltransferase complex / DNA duplex unwinding / establishment of cell polarity / actin filament bundle / subtelomeric heterochromatin formation / protein secretion / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / endocytosis / double-strand break repair / chromatin organization / histone binding / transcription by RNA polymerase II / chromosome, telomeric region / cytoskeleton / hydrolase activity / chromatin remodeling / DNA repair / mRNA binding / DNA-templated transcription / DNA damage response / chromatin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Nucleotidyltransferase; domain 5 - #580 / DNA helicase Ino80 / DBINO domain profile. / DBINO domain / DNA-binding domain / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / ATPase, substrate binding domain, subdomain 4 ...Nucleotidyltransferase; domain 5 - #580 / DNA helicase Ino80 / DBINO domain profile. / DBINO domain / DNA-binding domain / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / Helicase conserved C-terminal domain / ATPase, nucleotide binding domain / helicase superfamily c-terminal domain / Nucleotidyltransferase; domain 5 / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / LATRUNCULIN A / Chromatin-remodeling ATPase INO80 / Actin / Actin-related protein 4 / Actin-like protein ARP8
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4 Å
AuthorsKnoll, K.R. / Eustermann, S. / Hopfner, K.P.
Funding support3items
OrganizationGrant numberCountry
German Research FoundationGRK1721
German Research FoundationGRK1721
European Research CouncilATMMACHINE
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: The nuclear actin-containing Arp8 module is a linker DNA sensor driving INO80 chromatin remodeling.
Authors: Knoll, K.R. / Eustermann, S. / Niebauer, V. / Oberbeckmann, E. / Stoehr, G. / Schall, K. / Tosi, A. / Schwarz, M. / Buchfellner, A. / Korber, P. / Hopfner, K.P.
History
DepositionMar 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / 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
Revision 1.2Sep 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_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: Actin-related protein 4
B: Actin-related protein 4
C: Actin
D: Actin
E: Actin-like protein ARP8
F: Actin-like protein ARP8
G: Putative DNA helicase INO80
H: Putative DNA helicase INO80
hetero molecules


Theoretical massNumber of molelcules
Total (without water)376,33518
Polymers373,3038
Non-polymers3,03210
Water0
1
A: Actin-related protein 4
D: Actin
F: Actin-like protein ARP8
H: Putative DNA helicase INO80
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,1679
Polymers186,6514
Non-polymers1,5165
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13250 Å2
ΔGint-84 kcal/mol
Surface area62490 Å2
MethodPISA
2
B: Actin-related protein 4
C: Actin
E: Actin-like protein ARP8
G: Putative DNA helicase INO80
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,1679
Polymers186,6514
Non-polymers1,5165
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13450 Å2
ΔGint-83 kcal/mol
Surface area62450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.294, 263.909, 241.402
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 F and (resseq 257:299 or resseq 301:302 or resseq...
21(chain E and (resseq 257:299 or resseq 301:302 or resseq...
12(chain A and (resseq 15:59 or resseq 61:171 or (resid...
22(chain B and (resseq 15:59 or resseq 61:171 or (resid...
13(chain C and ((resid 5 and (name N or name...
23(chain D and ((resid 5 and (name O or name...
14(chain H and (resseq 472 or resseq 474:481 or resseq 483:557))
24(chain G and (resseq 472 or resseq 474:481 or resseq 483:557))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNLYSLYS(chain F and (resseq 257:299 or resseq 301:302 or resseq...FF257 - 2994 - 46
121TRPTRPLEULEU(chain F and (resseq 257:299 or resseq 301:302 or resseq...FF301 - 30248 - 49
131GLUGLUSERSER(chain F and (resseq 257:299 or resseq 301:302 or resseq...FF305 - 30752 - 54
141LEULEUMETMET(chain F and (resseq 257:299 or resseq 301:302 or resseq...FF315 - 33862 - 85
151TYRTYRTYRTYR(chain F and (resseq 257:299 or resseq 301:302 or resseq...FF34087
161ASNASNTYRTYR(chain F and (resseq 257:299 or resseq 301:302 or resseq...FF257 - 8814 - 628
171ASNASNTYRTYR(chain F and (resseq 257:299 or resseq 301:302 or resseq...FF257 - 8814 - 628
181ASNASNTYRTYR(chain F and (resseq 257:299 or resseq 301:302 or resseq...FF257 - 8814 - 628
191ASNASNTYRTYR(chain F and (resseq 257:299 or resseq 301:302 or resseq...FF257 - 8814 - 628
1101ASNASNTYRTYR(chain F and (resseq 257:299 or resseq 301:302 or resseq...FF257 - 8814 - 628
1111ASNASNTYRTYR(chain F and (resseq 257:299 or resseq 301:302 or resseq...FF257 - 8814 - 628
1121ASNASNTYRTYR(chain F and (resseq 257:299 or resseq 301:302 or resseq...FF257 - 8814 - 628
1131ASNASNTYRTYR(chain F and (resseq 257:299 or resseq 301:302 or resseq...FF257 - 8814 - 628
1141ASNASNTYRTYR(chain F and (resseq 257:299 or resseq 301:302 or resseq...FF257 - 8814 - 628
211ASNASNLYSLYS(chain E and (resseq 257:299 or resseq 301:302 or resseq...EE257 - 2994 - 46
221TRPTRPLEULEU(chain E and (resseq 257:299 or resseq 301:302 or resseq...EE301 - 30248 - 49
231GLUGLUSERSER(chain E and (resseq 257:299 or resseq 301:302 or resseq...EE305 - 30752 - 54
241LEULEUMETMET(chain E and (resseq 257:299 or resseq 301:302 or resseq...EE315 - 33862 - 85
251TYRTYRTYRTYR(chain E and (resseq 257:299 or resseq 301:302 or resseq...EE34087
261ASNASNTYRTYR(chain E and (resseq 257:299 or resseq 301:302 or resseq...EE257 - 8814 - 628
271ASNASNTYRTYR(chain E and (resseq 257:299 or resseq 301:302 or resseq...EE257 - 8814 - 628
281ASNASNTYRTYR(chain E and (resseq 257:299 or resseq 301:302 or resseq...EE257 - 8814 - 628
291ASNASNTYRTYR(chain E and (resseq 257:299 or resseq 301:302 or resseq...EE257 - 8814 - 628
2101ASNASNTYRTYR(chain E and (resseq 257:299 or resseq 301:302 or resseq...EE257 - 8814 - 628
2111ASNASNTYRTYR(chain E and (resseq 257:299 or resseq 301:302 or resseq...EE257 - 8814 - 628
2121ASNASNTYRTYR(chain E and (resseq 257:299 or resseq 301:302 or resseq...EE257 - 8814 - 628
2131ASNASNTYRTYR(chain E and (resseq 257:299 or resseq 301:302 or resseq...EE257 - 8814 - 628
2141ASNASNTYRTYR(chain E and (resseq 257:299 or resseq 301:302 or resseq...EE257 - 8814 - 628
112SERSERGLUGLU(chain A and (resseq 15:59 or resseq 61:171 or (resid...AA15 - 5915 - 59
122SERSERVALVAL(chain A and (resseq 15:59 or resseq 61:171 or (resid...AA61 - 17161 - 171
132ASPASPASPASP(chain A and (resseq 15:59 or resseq 61:171 or (resid...AA172172
142SERSERATPATP(chain A and (resseq 15:59 or resseq 61:171 or (resid...AA - J15 - 50215
152SERSERATPATP(chain A and (resseq 15:59 or resseq 61:171 or (resid...AA - J15 - 50215
162SERSERATPATP(chain A and (resseq 15:59 or resseq 61:171 or (resid...AA - J15 - 50215
172SERSERATPATP(chain A and (resseq 15:59 or resseq 61:171 or (resid...AA - J15 - 50215
182SERSERATPATP(chain A and (resseq 15:59 or resseq 61:171 or (resid...AA - J15 - 50215
192SERSERATPATP(chain A and (resseq 15:59 or resseq 61:171 or (resid...AA - J15 - 50215
212SERSERGLUGLU(chain B and (resseq 15:59 or resseq 61:171 or (resid...BB15 - 5915 - 59
222SERSERVALVAL(chain B and (resseq 15:59 or resseq 61:171 or (resid...BB61 - 17161 - 171
232ASPASPASPASP(chain B and (resseq 15:59 or resseq 61:171 or (resid...BB172172
242SERSERATPATP(chain B and (resseq 15:59 or resseq 61:171 or (resid...BB - L15 - 50215
252SERSERATPATP(chain B and (resseq 15:59 or resseq 61:171 or (resid...BB - L15 - 50215
262SERSERATPATP(chain B and (resseq 15:59 or resseq 61:171 or (resid...BB - L15 - 50215
272SERSERATPATP(chain B and (resseq 15:59 or resseq 61:171 or (resid...BB - L15 - 50215
282SERSERATPATP(chain B and (resseq 15:59 or resseq 61:171 or (resid...BB - L15 - 50215
292SERSERATPATP(chain B and (resseq 15:59 or resseq 61:171 or (resid...BB - L15 - 50215
113VALVALVALVAL(chain C and ((resid 5 and (name N or name...CC55
123VALVALCYSCYS(chain C and ((resid 5 and (name N or name...CC5 - 3745 - 374
133VALVALCYSCYS(chain C and ((resid 5 and (name N or name...CC5 - 3745 - 374
143VALVALCYSCYS(chain C and ((resid 5 and (name N or name...CC5 - 3745 - 374
153VALVALCYSCYS(chain C and ((resid 5 and (name N or name...CC5 - 3745 - 374
163VALVALCYSCYS(chain C and ((resid 5 and (name N or name...CC5 - 3745 - 374
213VALVALVALVAL(chain D and ((resid 5 and (name O or name...DD55
223VALVALCYSCYS(chain D and ((resid 5 and (name O or name...DD5 - 3745 - 374
233VALVALCYSCYS(chain D and ((resid 5 and (name O or name...DD5 - 3745 - 374
243VALVALCYSCYS(chain D and ((resid 5 and (name O or name...DD5 - 3745 - 374
253VALVALCYSCYS(chain D and ((resid 5 and (name O or name...DD5 - 3745 - 374
263VALVALCYSCYS(chain D and ((resid 5 and (name O or name...DD5 - 3745 - 374
114THRTHRTHRTHR(chain H and (resseq 472 or resseq 474:481 or resseq 483:557))HH47212
124THRTHRALAALA(chain H and (resseq 472 or resseq 474:481 or resseq 483:557))HH474 - 48114 - 21
134LYSLYSILEILE(chain H and (resseq 472 or resseq 474:481 or resseq 483:557))HH483 - 55723 - 97
214THRTHRTHRTHR(chain G and (resseq 472 or resseq 474:481 or resseq 483:557))GG47212
224THRTHRALAALA(chain G and (resseq 472 or resseq 474:481 or resseq 483:557))GG474 - 48114 - 21
234LYSLYSILEILE(chain G and (resseq 472 or resseq 474:481 or resseq 483:557))GG483 - 55723 - 97

NCS ensembles :
ID
1
2
3
4

-
Components

-
Protein , 4 types, 8 molecules ABCDEFGH

#1: Protein Actin-related protein 4 / Actin-like protein ARP4 / Actin-like protein 4


Mass: 54894.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Actin-related protein 4 (ATP bound)
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ARP4, ACT3, YJL081C, J1012 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P80428
#2: Protein Actin /


Mass: 41748.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Actin (ATP and Latrunculin A bound)
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ACT1, ABY1, END7, YFL039C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P60010
#3: Protein Actin-like protein ARP8


Mass: 71987.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal truncated construct of Actin-related protein 8(residues 255-881) in a nucleotide free state.
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ARP8, YOR141C, YOR3348C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q12386
#4: Protein Putative DNA helicase INO80 / Inositol-requiring protein 80


Mass: 18020.693 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: HSA/DBINO domain of the Ino80 protein (residues 461-598) carrying a C-terminal StrepTag.
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: INO80, YGL150C, G1880 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53115, DNA helicase

-
Non-polymers , 3 types, 10 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#7: Chemical ChemComp-LAR / LATRUNCULIN A / 4-(17-HYDROXY-5,12-DIMETHYL-3-OXO-2,16-DIOXABICYCLO[13.3.1]NONADECA-4,8,10-TRIEN-17-YL)-2-THIAZOLIDINONE / Latrunculin


Mass: 421.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H31NO5S / Comment: toxin*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.68 Å3/Da / Density % sol: 66.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate tribasic dihydrate, 18% (w/v) polyethylene glycol 3,350, latrunculin A solved in DMSO molar ration 1:1.5 (protein : latrunculin A)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→49.43 Å / Num. obs: 46724 / % possible obs: 99.9 % / Redundancy: 9.6 % / Biso Wilson estimate: 114.95 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.289 / Rpim(I) all: 0.098 / Rrim(I) all: 0.306 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
4-4.14101.3452.30.6880.4451.418100
15.49-49.438.40.07126.40.9960.0250.07596.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.47 Å49.4 Å
Translation6.47 Å49.4 Å

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimless0.5.27data scaling
PHASER2.6.1phasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AM6

4am6


Resolution: 4→49.399 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.54
RfactorNum. reflection% reflection
Rfree0.2422 2379 5.1 %
Rwork0.1927 --
obs0.1953 46675 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 282.05 Å2 / Biso mean: 121.6789 Å2 / Biso min: 34.6 Å2
Refinement stepCycle: final / Resolution: 4→49.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23029 0 186 0 23215
Biso mean--101.03 --
Num. residues----2898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223715
X-RAY DIFFRACTIONf_angle_d0.67532154
X-RAY DIFFRACTIONf_chiral_restr0.0633596
X-RAY DIFFRACTIONf_plane_restr0.0044105
X-RAY DIFFRACTIONf_dihedral_angle_d11.97714308
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11F5441X-RAY DIFFRACTION6.154TORSIONAL
12E5441X-RAY DIFFRACTION6.154TORSIONAL
21A3839X-RAY DIFFRACTION6.154TORSIONAL
22B3839X-RAY DIFFRACTION6.154TORSIONAL
31C3317X-RAY DIFFRACTION6.154TORSIONAL
32D3317X-RAY DIFFRACTION6.154TORSIONAL
41H842X-RAY DIFFRACTION6.154TORSIONAL
42G842X-RAY DIFFRACTION6.154TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.0001-4.08170.30761380.259725542692100
4.0817-4.17040.29911640.247825802744100
4.1704-4.26730.33391460.229525662712100
4.2673-4.3740.3071340.215625922726100
4.374-4.49220.2441140.207825952709100
4.4922-4.62430.25291260.196525992725100
4.6243-4.77340.2481300.190526042734100
4.7734-4.94390.24551490.186125522701100
4.9439-5.14160.24671550.19325752730100
5.1416-5.37530.23361320.190526122744100
5.3753-5.65840.27271460.21325882734100
5.6584-6.01230.26731610.198225832744100
6.0123-6.47560.23421230.193326242747100
6.4756-7.12550.2431310.191626402771100
7.1255-8.15260.22081310.170526312762100
8.1526-10.25630.1871660.139226482814100
10.2563-49.40260.21051330.19452753288699

+
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