[English] 日本語
Yorodumi
- PDB-5mub: ACC1 Fab fragment in complex with citrullinated C1 epitope of CII... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mub
TitleACC1 Fab fragment in complex with citrullinated C1 epitope of CII (CG05)
Components
  • (ACC1 Fab fragment heavy chain) x 2
  • ACC1 Fab fragment light chain
  • triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II
KeywordsIMMUNE SYSTEM / anti-citrullinated protein antibody (ACPA) / Fab fragment / collagen type II / citrullinated triple-helical C1 epitope
Function / homology
Function and homology information


Non-integrin membrane-ECM interactions / Extracellular matrix organization / NCAM1 interactions / Signaling by PDGF / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / collagen type II trimer / collagen type XI trimer / anterior head development / MET activates PTK2 signaling ...Non-integrin membrane-ECM interactions / Extracellular matrix organization / NCAM1 interactions / Signaling by PDGF / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / collagen type II trimer / collagen type XI trimer / anterior head development / MET activates PTK2 signaling / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / embryonic skeletal joint morphogenesis / otic vesicle development / ECM proteoglycans / limb bud formation / proteoglycan metabolic process / limb morphogenesis / platelet-derived growth factor binding / extracellular matrix structural constituent conferring tensile strength / Integrin cell surface interactions / notochord development / cartilage development involved in endochondral bone morphogenesis / MHC class II protein binding / cellular response to BMP stimulus / tissue homeostasis / endochondral ossification / collagen trimer / skeletal system morphogenesis / collagen fibril organization / cartilage development / proteoglycan binding / inner ear morphogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cartilage condensation / roof of mouth development / inner ear development / basement membrane / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / chondrocyte differentiation / heart morphogenesis / extrinsic apoptotic signaling pathway in absence of ligand / visual perception / extracellular matrix / ossification / skeletal system development / central nervous system development / sensory perception of sound / bone development / regulation of gene expression / collagen-containing extracellular matrix / protein homodimerization activity / extracellular space / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / : / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain ...Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / : / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Collagen alpha-1(II) chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsDobritzsch, D. / Holmdahl, R. / Ge, C.
Funding support Sweden, 5items
OrganizationGrant numberCountry
Swedish Foundation for Strategic ResearchRBa08-0047 Sweden
Swedish Foundation for Strategic ResearchRB13-015 Sweden
Knut and Alice Wallenberg FoundationKAW 2010.0148 Sweden
Swedish Research CouncilK2011-52X-07931-25-5, 2015-02662, K2009-75SX-21029-01-3, K2012-75SX-22072-01-3 Sweden
European UnionIMI 115142
CitationJournal: JCI Insight / Year: 2017
Title: Anti-citrullinated protein antibodies cause arthritis by cross-reactivity to joint cartilage.
Authors: Ge, C. / Tong, D. / Liang, B. / Lonnblom, E. / Schneider, N. / Hagert, C. / Viljanen, J. / Ayoglu, B. / Stawikowska, R. / Nilsson, P. / Fields, G.B. / Skogh, T. / Kastbom, A. / Kihlberg, J. ...Authors: Ge, C. / Tong, D. / Liang, B. / Lonnblom, E. / Schneider, N. / Hagert, C. / Viljanen, J. / Ayoglu, B. / Stawikowska, R. / Nilsson, P. / Fields, G.B. / Skogh, T. / Kastbom, A. / Kihlberg, J. / Burkhardt, H. / Dobritzsch, D. / Holmdahl, R.
History
DepositionJan 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_torsion / struct_conn / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_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 2.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ACC1 Fab fragment heavy chain
B: ACC1 Fab fragment light chain
X: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II
C: ACC1 Fab fragment heavy chain
D: ACC1 Fab fragment light chain
E: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II
F: ACC1 Fab fragment heavy chain
G: ACC1 Fab fragment light chain
H: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II
I: ACC1 Fab fragment heavy chain
J: ACC1 Fab fragment light chain
K: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II
L: ACC1 Fab fragment heavy chain
M: ACC1 Fab fragment light chain
N: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II
O: ACC1 Fab fragment heavy chain
P: ACC1 Fab fragment light chain
Q: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II
R: ACC1 Fab fragment heavy chain
S: ACC1 Fab fragment light chain
T: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II
U: ACC1 Fab fragment heavy chain
V: ACC1 Fab fragment light chain
W: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II


Theoretical massNumber of molelcules
Total (without water)401,15324
Polymers401,15324
Non-polymers00
Water00
1
A: ACC1 Fab fragment heavy chain
B: ACC1 Fab fragment light chain
X: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II


Theoretical massNumber of molelcules
Total (without water)50,0913
Polymers50,0913
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-27 kcal/mol
Surface area19590 Å2
MethodPISA
2
C: ACC1 Fab fragment heavy chain
D: ACC1 Fab fragment light chain
E: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II


Theoretical massNumber of molelcules
Total (without water)50,0913
Polymers50,0913
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-25 kcal/mol
Surface area19480 Å2
MethodPISA
3
F: ACC1 Fab fragment heavy chain
G: ACC1 Fab fragment light chain
H: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II


Theoretical massNumber of molelcules
Total (without water)50,3053
Polymers50,3053
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-26 kcal/mol
Surface area19570 Å2
MethodPISA
4
I: ACC1 Fab fragment heavy chain
J: ACC1 Fab fragment light chain
K: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II


Theoretical massNumber of molelcules
Total (without water)50,0913
Polymers50,0913
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-26 kcal/mol
Surface area19370 Å2
MethodPISA
5
L: ACC1 Fab fragment heavy chain
M: ACC1 Fab fragment light chain
N: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II


Theoretical massNumber of molelcules
Total (without water)50,0913
Polymers50,0913
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-27 kcal/mol
Surface area19500 Å2
MethodPISA
6
O: ACC1 Fab fragment heavy chain
P: ACC1 Fab fragment light chain
Q: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II


Theoretical massNumber of molelcules
Total (without water)50,0913
Polymers50,0913
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-26 kcal/mol
Surface area19260 Å2
MethodPISA
7
R: ACC1 Fab fragment heavy chain
S: ACC1 Fab fragment light chain
T: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II


Theoretical massNumber of molelcules
Total (without water)50,3053
Polymers50,3053
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-28 kcal/mol
Surface area19830 Å2
MethodPISA
8
U: ACC1 Fab fragment heavy chain
V: ACC1 Fab fragment light chain
W: triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II


Theoretical massNumber of molelcules
Total (without water)50,0913
Polymers50,0913
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-27 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.286, 155.099, 156.266
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22F
13A
23I
14A
24L
15A
25O
16A
26R
17A
27U
18B
28D
19B
29G
110B
210J
111B
211M
112B
212P
113B
213S
114B
214V
115C
215F
116C
216I
117C
217L
118C
218O
119C
219R
120C
220U
121D
221G
122D
222J
123D
223M
124D
224P
125D
225S
126D
226V
127F
227I
128F
228L
129F
229O
130F
230R
131F
231U
132G
232J
133G
233M
134G
234P
135G
235S
136G
236V
137I
237L
138I
238O
139I
239R
140I
240U
141J
241M
142J
242P
143J
243S
144J
244V
145L
245O
146L
246R
147L
247U
148M
248P
149M
249S
150M
250V
151O
251R
152O
252U
153P
253S
154P
254V
155R
255U
156S
256V

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUPROPROAA1 - 2181 - 218
21GLUGLUPROPROCD1 - 2181 - 218
12GLUGLUPROPROAA1 - 2181 - 218
22GLUGLUPROPROFG1 - 2181 - 218
13GLUGLUPROPROAA1 - 2181 - 218
23GLUGLUPROPROIJ1 - 2181 - 218
14GLUGLUPROPROAA1 - 2181 - 218
24GLUGLUPROPROLM1 - 2181 - 218
15GLUGLUPROPROAA1 - 2181 - 218
25GLUGLUPROPROOP1 - 2181 - 218
16GLUGLUGLYGLYAA1 - 2171 - 217
26GLUGLUGLYGLYRS1 - 2171 - 217
17GLUGLUPROPROAA1 - 2181 - 218
27GLUGLUPROPROUV1 - 2181 - 218
18ASPASPGLUGLUBB1 - 2171 - 217
28ASPASPGLUGLUDE1 - 2171 - 217
19ASPASPGLUGLUBB1 - 2171 - 217
29ASPASPGLUGLUGH1 - 2171 - 217
110ASPASPGLUGLUBB1 - 2171 - 217
210ASPASPGLUGLUJK1 - 2171 - 217
111ASPASPGLUGLUBB1 - 2171 - 217
211ASPASPGLUGLUMN1 - 2171 - 217
112ASPASPGLUGLUBB1 - 2171 - 217
212ASPASPGLUGLUPQ1 - 2171 - 217
113ASPASPGLUGLUBB1 - 2171 - 217
213ASPASPGLUGLUST1 - 2171 - 217
114ASPASPGLUGLUBB1 - 2171 - 217
214ASPASPGLUGLUVW1 - 2171 - 217
115GLUGLUGLYGLYCD1 - 2171 - 217
215GLUGLUGLYGLYFG1 - 2171 - 217
116GLUGLUPROPROCD1 - 2181 - 218
216GLUGLUPROPROIJ1 - 2181 - 218
117GLUGLUPROPROCD1 - 2181 - 218
217GLUGLUPROPROLM1 - 2181 - 218
118GLUGLUPROPROCD1 - 2181 - 218
218GLUGLUPROPROOP1 - 2181 - 218
119GLUGLUPROPROCD1 - 2181 - 218
219GLUGLUPROPRORS1 - 2181 - 218
120GLUGLUPROPROCD1 - 2181 - 218
220GLUGLUPROPROUV1 - 2181 - 218
121ASPASPGLUGLUDE1 - 2171 - 217
221ASPASPGLUGLUGH1 - 2171 - 217
122ASPASPGLUGLUDE1 - 2171 - 217
222ASPASPGLUGLUJK1 - 2171 - 217
123ASPASPGLUGLUDE1 - 2171 - 217
223ASPASPGLUGLUMN1 - 2171 - 217
124ASPASPGLUGLUDE1 - 2171 - 217
224ASPASPGLUGLUPQ1 - 2171 - 217
125ASPASPGLUGLUDE1 - 2171 - 217
225ASPASPGLUGLUST1 - 2171 - 217
126ASPASPGLUGLUDE1 - 2171 - 217
226ASPASPGLUGLUVW1 - 2171 - 217
127GLUGLUPROPROFG1 - 2181 - 218
227GLUGLUPROPROIJ1 - 2181 - 218
128GLUGLUGLYGLYFG1 - 2171 - 217
228GLUGLUGLYGLYLM1 - 2171 - 217
129GLUGLUPROPROFG1 - 2181 - 218
229GLUGLUPROPROOP1 - 2181 - 218
130GLUGLUILEILEFG1 - 2201 - 220
230GLUGLUILEILERS1 - 2201 - 220
131GLUGLUPROPROFG1 - 2181 - 218
231GLUGLUPROPROUV1 - 2181 - 218
132ASPASPGLUGLUGH1 - 2171 - 217
232ASPASPGLUGLUJK1 - 2171 - 217
133ASPASPGLUGLUGH1 - 2171 - 217
233ASPASPGLUGLUMN1 - 2171 - 217
134ASPASPGLUGLUGH1 - 2171 - 217
234ASPASPGLUGLUPQ1 - 2171 - 217
135ASPASPGLUGLUGH1 - 2171 - 217
235ASPASPGLUGLUST1 - 2171 - 217
136ASPASPGLUGLUGH1 - 2171 - 217
236ASPASPGLUGLUVW1 - 2171 - 217
137GLUGLUPROPROIJ1 - 2181 - 218
237GLUGLUPROPROLM1 - 2181 - 218
138GLUGLUPROPROIJ1 - 2181 - 218
238GLUGLUPROPROOP1 - 2181 - 218
139GLUGLUGLYGLYIJ1 - 2171 - 217
239GLUGLUGLYGLYRS1 - 2171 - 217
140GLUGLUPROPROIJ1 - 2181 - 218
240GLUGLUPROPROUV1 - 2181 - 218
141ASPASPGLUGLUJK1 - 2171 - 217
241ASPASPGLUGLUMN1 - 2171 - 217
142ASPASPGLUGLUJK1 - 2171 - 217
242ASPASPGLUGLUPQ1 - 2171 - 217
143ASPASPGLUGLUJK1 - 2171 - 217
243ASPASPGLUGLUST1 - 2171 - 217
144ASPASPGLUGLUJK1 - 2171 - 217
244ASPASPGLUGLUVW1 - 2171 - 217
145GLUGLUPROPROLM1 - 2181 - 218
245GLUGLUPROPROOP1 - 2181 - 218
146GLUGLUPROPROLM1 - 2181 - 218
246GLUGLUPROPRORS1 - 2181 - 218
147GLUGLUPROPROLM1 - 2181 - 218
247GLUGLUPROPROUV1 - 2181 - 218
148ASPASPGLUGLUMN1 - 2171 - 217
248ASPASPGLUGLUPQ1 - 2171 - 217
149ASPASPGLUGLUMN1 - 2171 - 217
249ASPASPGLUGLUST1 - 2171 - 217
150ASPASPGLUGLUMN1 - 2171 - 217
250ASPASPGLUGLUVW1 - 2171 - 217
151GLUGLUPROPROOP1 - 2181 - 218
251GLUGLUPROPRORS1 - 2181 - 218
152GLUGLUPROPROOP1 - 2181 - 218
252GLUGLUPROPROUV1 - 2181 - 218
153ASPASPGLUGLUPQ1 - 2171 - 217
253ASPASPGLUGLUST1 - 2171 - 217
154ASPASPGLUGLUPQ1 - 2171 - 217
254ASPASPGLUGLUVW1 - 2171 - 217
155GLUGLUGLYGLYRS1 - 2171 - 217
255GLUGLUGLYGLYUV1 - 2171 - 217
156ASPASPGLUGLUST1 - 2171 - 217
256ASPASPGLUGLUVW1 - 2171 - 217

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56

-
Components

#1: Antibody
ACC1 Fab fragment heavy chain


Mass: 23353.164 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: B cell hybridoma / Strain: B10.RIII.Cia5
#2: Antibody
ACC1 Fab fragment light chain


Mass: 23721.199 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: B cell hybridoma / Strain: B10.RIII.Cia5
#3: Protein/peptide
triple-helical peptide containing the citrullinated C1 epitope of collagen type II,Collagen alpha-1(II) chain,triple-helical peptide containing the citrullinated C1 epitope of collagen type II / Alpha-1 type II collagen


Mass: 3016.176 Da / Num. of mol.: 8 / Source method: obtained synthetically
Details: the synthesized peptide is homotrimeric and triple-helical in solution, but bound as single alpha-chain to the ACC1 Fab fragment
Source: (synth.) Mus musculus (house mouse) / References: UniProt: P28481
#4: Antibody ACC1 Fab fragment heavy chain


Mass: 23567.428 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: B cell hybridoma / Strain: B10.RIII.Cia5

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% (w/v) PEG 3350, 0.1 M Bistris-Propane pH 6.5, 0.2 M NaBr

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.1→78.14 Å / Num. obs: 65914 / % possible obs: 100 % / Redundancy: 4.7 % / Biso Wilson estimate: 31.8 Å2 / Rmerge(I) obs: 0.153 / Net I/σ(I): 10.1
Reflection shellResolution: 3.1→3.17 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.807 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4370 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MU0

5mu0


Resolution: 3.1→78.14 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.873 / SU B: 69.143 / SU ML: 0.492 / Cross valid method: THROUGHOUT / ESU R Free: 0.545 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26396 3245 4.9 %RANDOM
Rwork0.23133 ---
obs0.23296 62669 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.108 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2--1.78 Å2-0 Å2
3----1.31 Å2
Refinement stepCycle: 1 / Resolution: 3.1→78.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26877 0 0 0 26877
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227531
X-RAY DIFFRACTIONr_bond_other_d0.0020.0225180
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.94737407
X-RAY DIFFRACTIONr_angle_other_deg1.646358309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.98553516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27524.4441080
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.813154342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.12915112
X-RAY DIFFRACTIONr_chiral_restr0.1150.24199
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02131047
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026121
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1453.92514154
X-RAY DIFFRACTIONr_mcbond_other1.1453.92514154
X-RAY DIFFRACTIONr_mcangle_it1.9915.88717640
X-RAY DIFFRACTIONr_mcangle_other1.9915.88717641
X-RAY DIFFRACTIONr_scbond_it0.9923.97213377
X-RAY DIFFRACTIONr_scbond_other0.9923.97213377
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7265.92419768
X-RAY DIFFRACTIONr_long_range_B_refined3.09844.11528159
X-RAY DIFFRACTIONr_long_range_B_other3.09844.11528160
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A130760.06
12C130760.06
21A130600.05
22F130600.05
31A131580.05
32I131580.05
41A130780.05
42L130780.05
51A129640.05
52O129640.05
61A130440.06
62R130440.06
71A130520.07
72U130520.07
81B133740.05
82D133740.05
91B134320.05
92G134320.05
101B135180.03
102J135180.03
111B134320.05
112M134320.05
121B133480.06
122P133480.06
131B134080.05
132S134080.05
141B134420.04
142V134420.04
151C129500.06
152F129500.06
161C131020.05
162I131020.05
171C130280.06
172L130280.06
181C129580.05
182O129580.05
191C130000.06
192R130000.06
201C129920.07
202U129920.07
211D133080.06
212G133080.06
221D133280.05
222J133280.05
231D133640.06
232M133640.06
241D132680.07
242P132680.07
251D133300.06
252S133300.06
261D132460.06
262V132460.06
271F130520.05
272I130520.05
281F129980.06
282L129980.06
291F129880.05
292O129880.05
301F132380.04
302R132380.04
311F131200.06
312U131200.06
321G134290.05
322J134290.05
331G133510.06
332M133510.06
341G133290.07
342P133290.07
351G133530.06
352S133530.06
361G132790.06
362V132790.06
371I130400.06
372L130400.06
381I130420.04
382O130420.04
391I130180.06
392R130180.06
401I130580.07
402U130580.07
411J133640.05
412M133640.05
421J133460.06
422P133460.06
431J133660.06
432S133660.06
441J133760.05
442V133760.05
451L130220.05
452O130220.05
461L131100.06
462R131100.06
471L130540.07
472U130540.07
481M133020.06
482P133020.06
491M133760.06
492S133760.06
501M132740.06
502V132740.06
511O129760.05
512R129760.05
521O129900.05
522U129900.05
531P133520.07
532S133520.07
541P132060.07
542V132060.07
551R131660.06
552U131660.06
561S132320.06
562V132320.06
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 221 -
Rwork0.321 4582 -
obs--99.96 %
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)
11.9632-0.7469-0.37474.95731.74721.7169-0.2201-0.2369-0.21780.10570.05660.17350.29390.31150.16350.09980.04120.03240.20740.07810.0415-6.8006-40.390636.03
21.67580.1019-0.25684.36510.52872.4274-0.12640.2224-0.1376-0.42890.104-0.14970.17550.46020.02240.07930.05970.04040.32160.03520.03933.1431-38.759520.5693
314.7175.4889-5.3323.7149-0.91632.623-0.0688-0.68850.0863-0.08290.352-0.383-0.00810.6295-0.28320.35870.0735-0.08380.5107-0.1180.44814.5296-15.644443.557
40.2927-0.14780.08584.8974-2.95893.66480.0234-0.042-0.0713-0.12590.19990.72430.0033-0.4689-0.22340.0604-0.00780.0360.213-0.10130.5496-40.706-15.461643.6939
51.28890.9729-0.04415.1072-1.39712.66410.0415-0.0020.20050.4344-0.05560.0029-0.04360.37310.01420.11970.00350.09580.1915-0.08540.2185-24.2038-18.670251.2736
62.0054-0.28243.056917.9276-2.11934.8225-0.20460.05510.3803-0.6452-0.3552-0.1458-0.22190.13220.55980.4120.1015-0.0780.3705-0.04730.5505-30.59229.288236.5748
72.34740.5467-2.36360.8391-0.73544.14820.1964-0.01230.2996-0.03210.0110.0873-0.45490.1554-0.20740.17770.0075-0.06780.1881-0.12350.3221-61.5693-45.701831.4534
81.86660.709-1.40492.9502-1.56253.88930.03470.0151-0.1934-0.0334-0.1817-0.03490.13130.53140.1470.09850.1245-0.08820.2655-0.09470.1018-51.0887-60.285727.9926
93.3915-1.942-5.98821.14473.427410.7052-0.4883-0.1966-0.36870.2844-0.0220.24560.63930.42420.51030.5674-0.16440.06930.6093-0.10750.5812-79.4235-64.641742.7227
104.0439-0.07770.85461.8193-0.2021.60020.09080.1829-0.0311-0.167-0.1693-0.09840.03720.22550.07860.16530.10110.04630.11760.03170.0206-23.5954-67.910744.0494
114.32330.25540.4171.8369-0.52492.5395-0.0818-0.2243-0.21990.30950.0285-0.09040.120.30720.05330.20690.13550.03680.12690.04610.0286-22.3605-74.829860.9198
128.0443-3.0572-4.663919.28852.19222.75440.27160.20680.2405-0.642-0.02640.4454-0.1254-0.2238-0.24510.5804-0.1391-0.23260.6220.07640.5503-45.2073-85.775540.4844
136.17880.025-2.74771.0243-0.83682.2337-0.37830.9567-0.2819-0.37770.07160.20870.6356-0.57780.30670.689-0.20660.04470.4128-0.08270.4247-46.7377-11.88031.0859
145.87781.3303-1.66292.9709-0.56811.8702-0.186-0.33160.4763-0.01550.14530.16770.0586-0.0260.04070.3520.0993-0.05060.20880.00930.2936-48.5636-2.00616.675
1513.7498-6.8227-6.30017.34427.3527.4018-0.7851-0.5744-0.71560.06780.8688-0.009-0.00930.9065-0.08370.5214-0.05640.09860.42420.09920.6162-26.0035.6841-5.1029
162.3683-1.1312-1.78414.35262.63.907-0.0326-0.85840.36990.09890.3656-0.3362-0.16261.0305-0.3330.1164-0.00440.02430.583-0.00510.1504-32.0814-58.883987.2384
173.2120.3878-0.63074.08452.30573.7549-0.0213-0.41020.2602-0.02330.10360.2802-0.33040.2684-0.08230.16330.03920.0690.30940.09220.1653-49.5013-55.409192.773
185.7540.0694-8.98542.05393.60520.8903-0.26620.40610.2314-0.14950.22610.3743-0.0193-0.18680.04010.56520.02660.13550.2776-0.03880.6647-41.1376-83.834380.9983
191.6739-0.98080.99664.0171-2.27662.3683-0.12280.00840.29810.126-0.0479-0.017-0.4843-0.11150.17060.24790.0260.03460.2282-0.08210.2086-69.9463-35.790674.5587
201.6654-0.35370.41254.4762-0.86242.34380.06730.33840.0042-0.5312-0.13870.0432-0.0503-0.20960.07140.13350.09230.01840.2902-0.08440.1526-78.1951-41.180459.1903
2110.48956.53211.42345.81671.75820.62880.2146-1.36140.05240.3461-0.38030.39290.13590.03460.16580.3297-0.0002-0.02370.65810.24440.5633-77.8264-62.247284.3369
224.16461.53032.59651.28590.93614.26580.41550.3044-0.6333-0.0059-0.15240.14080.5564-0.0796-0.26310.25520.018-0.05790.4089-0.090.3957-12.6793-36.2925-6.4442
234.29111.30311.59862.2580.89912.33910.08520.64410.263-0.0965-0.13530.2447-0.3758-0.29220.05010.34450.08620.04350.61380.0090.1887-21.0879-21.679-13.6094
241.60260.4782-1.6920.45940.65816.84570.0965-0.67790.15710.3165-0.3512-0.01480.7511-0.12890.25470.57580.0271-0.08940.6308-0.15230.66167.6724-18.59620.8358
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 218
2X-RAY DIFFRACTION2B1 - 217
3X-RAY DIFFRACTION3X11 - 21
4X-RAY DIFFRACTION4C1 - 218
5X-RAY DIFFRACTION5D1 - 217
6X-RAY DIFFRACTION6E13 - 21
7X-RAY DIFFRACTION7F1 - 220
8X-RAY DIFFRACTION8G1 - 217
9X-RAY DIFFRACTION9H13 - 21
10X-RAY DIFFRACTION10I1 - 218
11X-RAY DIFFRACTION11J1 - 217
12X-RAY DIFFRACTION12K13 - 22
13X-RAY DIFFRACTION13L1 - 218
14X-RAY DIFFRACTION14M1 - 217
15X-RAY DIFFRACTION15N13 - 21
16X-RAY DIFFRACTION16O1 - 218
17X-RAY DIFFRACTION17P1 - 217
18X-RAY DIFFRACTION18Q14 - 21
19X-RAY DIFFRACTION19R1 - 220
20X-RAY DIFFRACTION20S1 - 217
21X-RAY DIFFRACTION21T10 - 21
22X-RAY DIFFRACTION22U1 - 218
23X-RAY DIFFRACTION23V1 - 217
24X-RAY DIFFRACTION24W13 - 21

+
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