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- PDB-5mv3: ACC1 Fab fragment in complex with CII583-591 (CG10) -

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Basic information

Entry
Database: PDB / ID: 5mv3
TitleACC1 Fab fragment in complex with CII583-591 (CG10)
Components
  • (heavy chain of ACC1 Fab fragment) x 2
  • light chain of ACC1 Fab fragment
  • synthetic peptide containing the CII583-591 epitope of collagen type II,Collagen alpha-1(II) chain,synthetic peptide containing the CII583-591 epitope of collagen type II,
KeywordsIMMUNE SYSTEM / anti-citrullinated protein antibody (ACPA) / Fab fragment / collagen type II
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 / MET activates PTK2 signaling / anterior head development ...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 / MET activates PTK2 signaling / anterior head development / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / embryonic skeletal joint morphogenesis / otic vesicle development / ECM proteoglycans / proteoglycan metabolic process / extracellular matrix structural constituent conferring tensile strength / platelet-derived growth factor binding / Integrin cell surface interactions / cartilage development involved in endochondral bone morphogenesis / notochord development / limb bud formation / limb morphogenesis / tissue homeostasis / MHC class II protein binding / cellular response to BMP stimulus / endochondral ossification / collagen trimer / collagen fibril organization / cartilage development / skeletal system morphogenesis / proteoglycan binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / inner ear morphogenesis / 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 / central nervous system development / skeletal 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 / Collagen triple helix repeat ...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: 2.95 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 15, 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 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: heavy chain of ACC1 Fab fragment
B: light chain of ACC1 Fab fragment
X: synthetic peptide containing the CII583-591 epitope of collagen type II,Collagen alpha-1(II) chain,synthetic peptide containing the CII583-591 epitope of collagen type II,
C: heavy chain of ACC1 Fab fragment
D: light chain of ACC1 Fab fragment
E: synthetic peptide containing the CII583-591 epitope of collagen type II,Collagen alpha-1(II) chain,synthetic peptide containing the CII583-591 epitope of collagen type II,
F: heavy chain of ACC1 Fab fragment
G: light chain of ACC1 Fab fragment
H: synthetic peptide containing the CII583-591 epitope of collagen type II,Collagen alpha-1(II) chain,synthetic peptide containing the CII583-591 epitope of collagen type II,
I: heavy chain of ACC1 Fab fragment
J: light chain of ACC1 Fab fragment
K: synthetic peptide containing the CII583-591 epitope of collagen type II,Collagen alpha-1(II) chain,synthetic peptide containing the CII583-591 epitope of collagen type II,
L: heavy chain of ACC1 Fab fragment
M: light chain of ACC1 Fab fragment
N: synthetic peptide containing the CII583-591 epitope of collagen type II,Collagen alpha-1(II) chain,synthetic peptide containing the CII583-591 epitope of collagen type II,
O: heavy chain of ACC1 Fab fragment
P: light chain of ACC1 Fab fragment
Q: synthetic peptide containing the CII583-591 epitope of collagen type II,Collagen alpha-1(II) chain,synthetic peptide containing the CII583-591 epitope of collagen type II,
R: heavy chain of ACC1 Fab fragment
S: light chain of ACC1 Fab fragment
T: synthetic peptide containing the CII583-591 epitope of collagen type II,Collagen alpha-1(II) chain,synthetic peptide containing the CII583-591 epitope of collagen type II,
U: heavy chain of ACC1 Fab fragment
V: light chain of ACC1 Fab fragment
W: synthetic peptide containing the CII583-591 epitope of collagen type II,Collagen alpha-1(II) chain,synthetic peptide containing the CII583-591 epitope of collagen type II,


Theoretical massNumber of molelcules
Total (without water)398,40124
Polymers398,40124
Non-polymers00
Water0
1
A: heavy chain of ACC1 Fab fragment
B: light chain of ACC1 Fab fragment
X: synthetic peptide containing the CII583-591 epitope of collagen type II,Collagen alpha-1(II) chain,synthetic peptide containing the CII583-591 epitope of collagen type II,


Theoretical massNumber of molelcules
Total (without water)49,7733
Polymers49,7733
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-36 kcal/mol
Surface area20150 Å2
MethodPISA
2
C: heavy chain of ACC1 Fab fragment
D: light chain of ACC1 Fab fragment
E: synthetic peptide containing the CII583-591 epitope of collagen type II,Collagen alpha-1(II) chain,synthetic peptide containing the CII583-591 epitope of collagen type II,


Theoretical massNumber of molelcules
Total (without water)49,7733
Polymers49,7733
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-32 kcal/mol
Surface area19870 Å2
MethodPISA
3
F: heavy chain of ACC1 Fab fragment
G: light chain of ACC1 Fab fragment
H: synthetic peptide containing the CII583-591 epitope of collagen type II,Collagen alpha-1(II) chain,synthetic peptide containing the CII583-591 epitope of collagen type II,


Theoretical massNumber of molelcules
Total (without water)49,7733
Polymers49,7733
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-32 kcal/mol
Surface area19940 Å2
MethodPISA
4
I: heavy chain of ACC1 Fab fragment
J: light chain of ACC1 Fab fragment
K: synthetic peptide containing the CII583-591 epitope of collagen type II,Collagen alpha-1(II) chain,synthetic peptide containing the CII583-591 epitope of collagen type II,


Theoretical massNumber of molelcules
Total (without water)49,7733
Polymers49,7733
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-36 kcal/mol
Surface area20130 Å2
MethodPISA
5
L: heavy chain of ACC1 Fab fragment
M: light chain of ACC1 Fab fragment
N: synthetic peptide containing the CII583-591 epitope of collagen type II,Collagen alpha-1(II) chain,synthetic peptide containing the CII583-591 epitope of collagen type II,


Theoretical massNumber of molelcules
Total (without water)49,9883
Polymers49,9883
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-34 kcal/mol
Surface area20300 Å2
MethodPISA
6
O: heavy chain of ACC1 Fab fragment
P: light chain of ACC1 Fab fragment
Q: synthetic peptide containing the CII583-591 epitope of collagen type II,Collagen alpha-1(II) chain,synthetic peptide containing the CII583-591 epitope of collagen type II,


Theoretical massNumber of molelcules
Total (without water)49,7733
Polymers49,7733
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-32 kcal/mol
Surface area19830 Å2
MethodPISA
7
R: heavy chain of ACC1 Fab fragment
S: light chain of ACC1 Fab fragment
T: synthetic peptide containing the CII583-591 epitope of collagen type II,Collagen alpha-1(II) chain,synthetic peptide containing the CII583-591 epitope of collagen type II,


Theoretical massNumber of molelcules
Total (without water)49,7733
Polymers49,7733
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-36 kcal/mol
Surface area19890 Å2
MethodPISA
8
U: heavy chain of ACC1 Fab fragment
V: light chain of ACC1 Fab fragment
W: synthetic peptide containing the CII583-591 epitope of collagen type II,Collagen alpha-1(II) chain,synthetic peptide containing the CII583-591 epitope of collagen type II,


Theoretical massNumber of molelcules
Total (without water)49,7733
Polymers49,7733
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-34 kcal/mol
Surface area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.353, 92.844, 121.706
Angle α, β, γ (deg.)92.50, 106.53, 104.31
Int Tables number1
Space group name H-MP1
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
115X
215E
116X
216H
117X
217K
118X
218N
119X
219Q
120X
220T
121X
221W
122C
222F
123C
223I
124C
224L
125C
225O
126C
226R
127C
227U
128D
228G
129D
229J
130D
230M
131D
231P
132D
232S
133D
233V
134E
234H
135E
235K
136E
236N
137E
237Q
138E
238T
139E
239W
140F
240I
141F
241L
142F
242O
143F
243R
144F
244U
145G
245J
146G
246M
147G
247P
148G
248S
149G
249V
150H
250K
151H
251N
152H
252Q
153H
253T
154H
254W
155I
255L
156I
256O
157I
257R
158I
258U
159J
259M
160J
260P
161J
261S
162J
262V
163K
263N
164K
264Q
165K
265T
166K
266W
167L
267O
168L
268R
169L
269U
170M
270P
171M
271S
172M
272V
173N
273Q
174N
274T
175N
275W
176O
276R
177O
277U
178P
278S
179P
279V
180Q
280T
181Q
281W
182R
282U
183S
283V
184T
284W

NCS domain segments:

Component-ID: 0 / Refine code: 0

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
16VALVALPROPROAA2 - 2182 - 218
26VALVALPROPRORS2 - 2182 - 218
17GLUGLUPROPROAA1 - 2181 - 218
27GLUGLUPROPROUV1 - 2181 - 218
18ASPASPASNASNBB1 - 2161 - 216
28ASPASPASNASNDE1 - 2161 - 216
19ASPASPASNASNBB1 - 2161 - 216
29ASPASPASNASNGH1 - 2161 - 216
110ASPASPCYSCYSBB1 - 2181 - 218
210ASPASPCYSCYSJK1 - 2181 - 218
111ASPASPCYSCYSBB1 - 2181 - 218
211ASPASPCYSCYSMN1 - 2181 - 218
112ASPASPASNASNBB1 - 2141 - 214
212ASPASPASNASNPQ1 - 2141 - 214
113ASPASPCYSCYSBB1 - 2181 - 218
213ASPASPCYSCYSST1 - 2181 - 218
114ASPASPCYSCYSBB1 - 2181 - 218
214ASPASPCYSCYSVW1 - 2181 - 218
115HYPHYPGLYGLYXC12 - 2212 - 22
215HYPHYPGLYGLYEF12 - 2212 - 22
116HYPHYPGLYGLYXC12 - 2212 - 22
216HYPHYPGLYGLYHI12 - 2212 - 22
117PROPROGLYGLYXC11 - 2211 - 22
217PROPROGLYGLYKL11 - 2211 - 22
118PROPROGLYGLYXC11 - 2211 - 22
218PROPROGLYGLYNO11 - 2211 - 22
119HYPHYPGLYGLYXC12 - 2212 - 22
219HYPHYPGLYGLYQR12 - 2212 - 22
120HYPHYPGLYGLYXC12 - 2212 - 22
220HYPHYPGLYGLYTU12 - 2212 - 22
121HYPHYPGLYGLYXC12 - 2212 - 22
221HYPHYPGLYGLYWX12 - 2212 - 22
122GLUGLUPROPROCD1 - 2181 - 218
222GLUGLUPROPROFG1 - 2181 - 218
123GLUGLUPROPROCD1 - 2181 - 218
223GLUGLUPROPROIJ1 - 2181 - 218
124GLUGLUPROPROCD1 - 2181 - 218
224GLUGLUPROPROLM1 - 2181 - 218
125GLUGLUPROPROCD1 - 2181 - 218
225GLUGLUPROPROOP1 - 2181 - 218
126VALVALPROPROCD2 - 2182 - 218
226VALVALPROPRORS2 - 2182 - 218
127GLUGLUPROPROCD1 - 2181 - 218
227GLUGLUPROPROUV1 - 2181 - 218
128ASPASPGLUGLUDE1 - 2171 - 217
228ASPASPGLUGLUGH1 - 2171 - 217
129ASPASPASNASNDE1 - 2161 - 216
229ASPASPASNASNJK1 - 2161 - 216
130ASPASPASNASNDE1 - 2161 - 216
230ASPASPASNASNMN1 - 2161 - 216
131ASPASPASNASNDE1 - 2141 - 214
231ASPASPASNASNPQ1 - 2141 - 214
132ASPASPASNASNDE1 - 2161 - 216
232ASPASPASNASNST1 - 2161 - 216
133ASPASPASNASNDE1 - 2161 - 216
233ASPASPASNASNVW1 - 2161 - 216
134HYPHYPGLYGLYEF12 - 2212 - 22
234HYPHYPGLYGLYHI12 - 2212 - 22
135HYPHYPGLYGLYEF12 - 2212 - 22
235HYPHYPGLYGLYKL12 - 2212 - 22
136HYPHYPGLYGLYEF12 - 2212 - 22
236HYPHYPGLYGLYNO12 - 2212 - 22
137HYPHYPGLYGLYEF12 - 2212 - 22
237HYPHYPGLYGLYQR12 - 2212 - 22
138HYPHYPGLYGLYEF12 - 2212 - 22
238HYPHYPGLYGLYTU12 - 2212 - 22
139HYPHYPGLYGLYEF12 - 2212 - 22
239HYPHYPGLYGLYWX12 - 2212 - 22
140GLUGLUPROPROFG1 - 2181 - 218
240GLUGLUPROPROIJ1 - 2181 - 218
141GLUGLUPROPROFG1 - 2181 - 218
241GLUGLUPROPROLM1 - 2181 - 218
142GLUGLUPROPROFG1 - 2181 - 218
242GLUGLUPROPROOP1 - 2181 - 218
143VALVALPROPROFG2 - 2182 - 218
243VALVALPROPRORS2 - 2182 - 218
144GLUGLUPROPROFG1 - 2181 - 218
244GLUGLUPROPROUV1 - 2181 - 218
145ASPASPASNASNGH1 - 2161 - 216
245ASPASPASNASNJK1 - 2161 - 216
146ASPASPASNASNGH1 - 2161 - 216
246ASPASPASNASNMN1 - 2161 - 216
147ASPASPASNASNGH1 - 2141 - 214
247ASPASPASNASNPQ1 - 2141 - 214
148ASPASPASNASNGH1 - 2161 - 216
248ASPASPASNASNST1 - 2161 - 216
149ASPASPASNASNGH1 - 2161 - 216
249ASPASPASNASNVW1 - 2161 - 216
150HYPHYPGLYGLYHI12 - 2212 - 22
250HYPHYPGLYGLYKL12 - 2212 - 22
151HYPHYPGLYGLYHI12 - 2212 - 22
251HYPHYPGLYGLYNO12 - 2212 - 22
152HYPHYPPROPROHI12 - 2312 - 23
252HYPHYPPROPROQR12 - 2312 - 23
153HYPHYPPROPROHI12 - 2312 - 23
253HYPHYPPROPROTU12 - 2312 - 23
154HYPHYPPROPROHI12 - 2312 - 23
254HYPHYPPROPROWX12 - 2312 - 23
155GLUGLUPROPROIJ1 - 2181 - 218
255GLUGLUPROPROLM1 - 2181 - 218
156GLUGLUPROPROIJ1 - 2181 - 218
256GLUGLUPROPROOP1 - 2181 - 218
157VALVALGLYGLYIJ2 - 2172 - 217
257VALVALGLYGLYRS2 - 2172 - 217
158GLUGLUPROPROIJ1 - 2181 - 218
258GLUGLUPROPROUV1 - 2181 - 218
159ASPASPCYSCYSJK1 - 2181 - 218
259ASPASPCYSCYSMN1 - 2181 - 218
160ASPASPASNASNJK1 - 2141 - 214
260ASPASPASNASNPQ1 - 2141 - 214
161ASPASPCYSCYSJK1 - 2181 - 218
261ASPASPCYSCYSST1 - 2181 - 218
162ASPASPCYSCYSJK1 - 2181 - 218
262ASPASPCYSCYSVW1 - 2181 - 218
163PROPROPROPROKL11 - 2311 - 23
263PROPROPROPRONO11 - 2311 - 23
164HYPHYPGLYGLYKL12 - 2212 - 22
264HYPHYPGLYGLYQR12 - 2212 - 22
165HYPHYPGLYGLYKL12 - 2212 - 22
265HYPHYPGLYGLYTU12 - 2212 - 22
166HYPHYPGLYGLYKL12 - 2212 - 22
266HYPHYPGLYGLYWX12 - 2212 - 22
167GLUGLUPROPROLM1 - 2181 - 218
267GLUGLUPROPROOP1 - 2181 - 218
168VALVALPROPROLM2 - 2182 - 218
268VALVALPROPRORS2 - 2182 - 218
169GLUGLUPROPROLM1 - 2181 - 218
269GLUGLUPROPROUV1 - 2181 - 218
170ASPASPASNASNMN1 - 2141 - 214
270ASPASPASNASNPQ1 - 2141 - 214
171ASPASPCYSCYSMN1 - 2181 - 218
271ASPASPCYSCYSST1 - 2181 - 218
172ASPASPCYSCYSMN1 - 2181 - 218
272ASPASPCYSCYSVW1 - 2181 - 218
173HYPHYPGLYGLYNO12 - 2212 - 22
273HYPHYPGLYGLYQR12 - 2212 - 22
174HYPHYPGLYGLYNO12 - 2212 - 22
274HYPHYPGLYGLYTU12 - 2212 - 22
175HYPHYPGLYGLYNO12 - 2212 - 22
275HYPHYPGLYGLYWX12 - 2212 - 22
176VALVALGLYGLYOP2 - 2172 - 217
276VALVALGLYGLYRS2 - 2172 - 217
177GLUGLUPROPROOP1 - 2181 - 218
277GLUGLUPROPROUV1 - 2181 - 218
178ASPASPASNASNPQ1 - 2141 - 214
278ASPASPASNASNST1 - 2141 - 214
179ASPASPASNASNPQ1 - 2141 - 214
279ASPASPASNASNVW1 - 2141 - 214
180HYPHYPPROPROQR12 - 2312 - 23
280HYPHYPPROPROTU12 - 2312 - 23
181HYPHYPPROPROQR12 - 2312 - 23
281HYPHYPPROPROWX12 - 2312 - 23
182VALVALPROPRORS2 - 2182 - 218
282VALVALPROPROUV2 - 2182 - 218
183ASPASPCYSCYSST1 - 2181 - 218
283ASPASPCYSCYSVW1 - 2181 - 218
184HYPHYPPROPROTU12 - 2312 - 23
284HYPHYPPROPROWX12 - 2312 - 23

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
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84

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Components

#1: Antibody
heavy chain of ACC1 Fab fragment


Mass: 23353.164 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: B cell hybridoma / Strain: B10.RIII.Cia5
#2: Antibody
light chain of ACC1 Fab fragment


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
synthetic peptide containing the CII583-591 epitope of collagen type II,Collagen alpha-1(II) chain,synthetic peptide containing the CII583-591 epitope of collagen type II, / Alpha-1 type II collagen


Mass: 2698.919 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 ACC1
Source: (synth.) Mus musculus (house mouse) / References: UniProt: P28481
#4: Antibody heavy chain of ACC1 Fab fragment


Mass: 23567.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: B cell hybridoma / Strain: B10.RIII.Cia5

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% (w/v) PEG3350, 0.1 M Bistris-Propane pH 7.0, 0.2 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.95→48.9 Å / Num. obs: 73522 / % possible obs: 99 % / Redundancy: 3.2 % / Biso Wilson estimate: 55.5 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.4
Reflection shellResolution: 2.95→3.01 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4569 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MU0
Resolution: 2.95→50.01 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.898 / SU B: 58.786 / SU ML: 0.453 / Cross valid method: THROUGHOUT / ESU R Free: 0.488 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26098 3639 4.9 %RANDOM
Rwork0.2015 ---
obs0.20442 69880 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.264 Å2
Baniso -1Baniso -2Baniso -3
1-2.49 Å2-1.85 Å20.35 Å2
2---1.66 Å21.05 Å2
3----0.29 Å2
Refinement stepCycle: 1 / Resolution: 2.95→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26921 0 0 0 26921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227593
X-RAY DIFFRACTIONr_bond_other_d0.0020.0225227
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.94637500
X-RAY DIFFRACTIONr_angle_other_deg1.004358464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.50753528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07624.4291077
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.699154351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.10415112
X-RAY DIFFRACTIONr_chiral_restr0.1110.24202
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02131086
X-RAY DIFFRACTIONr_gen_planes_other0.0030.026098
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_it0.9143.56914208
X-RAY DIFFRACTIONr_mcbond_other0.9143.56914207
X-RAY DIFFRACTIONr_mcangle_it1.6115.34917704
X-RAY DIFFRACTIONr_mcangle_other1.6115.34917705
X-RAY DIFFRACTIONr_scbond_it0.6973.56713385
X-RAY DIFFRACTIONr_scbond_other0.6973.56713386
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2395.33519797
X-RAY DIFFRACTIONr_long_range_B_refined2.59940.01728137
X-RAY DIFFRACTIONr_long_range_B_other2.59940.01928138
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)
11A16480.01
12C16480.01
21A16540.01
22F16540.01
31A16520.01
32I16520.01
41A16460.01
42L16460.01
51A16420.01
52O16420.01
61A16280.01
62R16280.01
71A15640.01
72U15640.01
81B16580.01
82D16580.01
91B16600.01
92G16600.01
101B16920.01
102J16920.01
111B16740.01
112M16740.01
121B16460.01
122P16460.01
131B16520.01
132S16520.01
141B16520.01
142V16520.01
151X520
152E520
161X520
162H520
171X580.01
172K580.01
181X620.01
182N620.01
191X580.01
192Q580.01
201X560
202T560
211X600
212W600
221C16560.01
222F16560.01
231C16680.01
232I16680.01
241C16720.01
242L16720.01
251C16540.01
252O16540.01
261C16360.01
262R16360.01
271C15640.01
272U15640.01
281D16620.01
282G16620.01
291D16660.01
292J16660.01
301D16800.01
302M16800.01
311D16400.01
312P16400.01
321D16460.01
322S16460.01
331D16180.01
332V16180.01
341E500
342H500
351E500
352K500
361E540
362N540
371E520
372Q520
381E520
382T520
391E500
392W500
401F16600.01
402I16600.01
411F16360.01
412L16360.01
421F16320.01
422O16320.01
431F16280.01
432R16280.01
441F15620.01
442U15620.01
451G16700.01
452J16700.01
461G16720.01
462M16720.01
471G16480.01
472P16480.01
481G16640.01
482S16640.01
491G16500.01
492V16500.01
501H540
502K540
511H540
512N540
521H580.01
522Q580.01
531H580
532T580
541H560
542W560
551I16640.01
552L16640.01
561I16560.01
562O16560.01
571I16340.01
572R16340.01
581I15500.01
582U15500.01
591J16960.01
592M16960.01
601J16620.01
602P16620.01
611J16720.01
612S16720.01
621J16620.01
622V16620.01
631K660.01
632N660.01
641K520.01
642Q520.01
651K540
652T540
661K520
662W520
671L16720.01
672O16720.01
681L16420.01
682R16420.01
691L15360.01
692U15360.01
701M16660.01
702P16660.01
711M16800.01
712S16800.01
721M16540.01
722V16540.01
731N560
732Q560
741N580
742T580
751N560
752W560
761O16260.01
762R16260.01
771O15400.01
772U15400.01
781P16520.01
782S16520.01
791P16320.01
792V16320.01
801Q580
802T580
811Q580.01
812W580.01
821R15560.01
822U15560.01
831S16760.01
832V16760.01
841T580
842W580
LS refinement shellResolution: 2.95→3.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 242 -
Rwork0.327 5212 -
obs--98.66 %
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)
19.46610.02941.8041.5828-0.20592.22-0.4302-0.84030.39070.51660.2016-0.191-0.19310.03670.22860.30150.0974-0.05520.1618-0.02910.062641.829920.286511.2489
27.71151.22032.44375.30941.15724.74970.055-1.2787-0.99720.42570.20560.55830.0088-0.8633-0.26060.12340.10040.16350.53360.28440.376115.54499.69337.3061
310.47354.6584.28733.37943.27388.0124-0.56461.93540.6484-0.07920.2884-0.0687-0.49951.15860.27620.3533-0.2526-0.15710.77990.34910.177341.575326.2583-14.5261
47.47851.13390.75491.7986-0.36633.483-0.24980.19930.0672-0.05130.18070.4707-0.3309-0.26730.06910.1490.0368-0.01510.04150.03150.143922.208918.9514-6.0297
53.27191.6224-3.9415.7892-1.72737.84230.059-0.0712-0.3532-0.68-0.4824-0.48880.80780.54230.42350.4010.2472-0.04630.1738-0.07580.280612.3042-47.3143-29.7741
61.79592.4025-1.00986.632-3.49313.66070.14690.1294-0.1283-0.858-0.6172-0.6850.3441.18180.47030.45040.26910.03140.67120.00210.216422.38-33.8255-38.6938
73.66380.56641.06138.9366-0.64763.98940.22370.1174-0.03720.28380.11820.9089-0.00790.0063-0.34190.06380.0618-0.03150.0676-0.06050.1922-2.8066-31.5239-28.2058
83.7039-0.2241-2.71262.0378-0.99266.50020.15370.44740.1777-0.8292-0.0977-0.17730.24290.7357-0.0560.4810.07190.09140.3846-0.04540.178219.8569-14.0902-51.6623
95.9645-2.0322-0.02676.521-0.29343.9912-0.04470.28830.4083-0.1581-0.023-0.5368-0.2238-0.02830.06780.1766-0.1219-0.020.1090.04880.24955.482925.684942.4876
102.8834-1.2717-0.71347.8491.18714.50630.54610.51670.0395-0.6374-0.43110.03710.2945-0.202-0.11490.27290.23210.08170.55130.13370.098619.0056-0.386228.6727
112.2651-0.2002-0.13468.57030.19890.8294-0.1166-0.1587-0.05140.9212-0.040.4692-0.108-0.32540.15660.3475-0.0946-0.00840.255-0.01930.1104-0.97938.330356.631
126.2077-1.0399-4.09463.69520.19586.1720.62480.37280.1567-0.1356-0.6344-0.65960.39960.69060.00960.34490.1874-0.0040.38560.09880.220226.4006-9.541139.5989
137.41332.00260.4861.4071-0.76432.3845-0.35070.5410.166-0.37460.2260.18360.1443-0.00660.12470.4717-0.0436-0.09680.10290.01120.0806-28.128611.9715-51.864
145.7354-0.76460.47783.2282-0.08236.9767-0.2590.4229-0.0183-0.18780.1968-0.26210.16020.46140.06210.188-0.0990.09690.1275-0.06220.14943.74489.1494-43.1525
156.947-0.29072.30022.3274-0.64625.7417-0.1187-1.33740.66480.0347-0.15530.57070.0084-0.98840.2740.28760.0365-0.04330.3517-0.210.2325-28.491220.0967-30.0629
167.30040.5311-3.31131.6157-0.25454.0626-0.18850.33240.5338-0.27910.2163-0.4825-0.45630.2464-0.02780.2907-0.0578-0.04930.155-0.04780.27797.624323.3739-37.6035
173.1733-1.4116-0.47325.55541.0586.73630.0674-0.2912-0.11510.724-0.45170.10360.2987-0.44320.38430.2323-0.2651-0.04490.34790.070.057244.2512-52.1895-15.204
182.3183-0.4964-1.18257.2348-0.25992.5790.2928-0.0475-0.02250.4479-0.42420.98430.086-0.18830.13140.1841-0.19870.12410.4363-0.2440.265323.5276-27.2403-8.6697
195.829-4.5370.30056.8904-1.05372.24560.36180.12970.4934-0.2548-0.2763-1.415-0.0357-0.158-0.08550.1214-0.1131-0.06440.19250.22320.515660.1849-33.3231-22.3848
203.3938-3.0213-1.6056.29792.4471.51780.3590.2060.26460.3479-0.5729-0.0769-0.0937-0.36420.21390.2732-0.1584-0.07020.3384-0.0020.234740.0764-22.4031-13.0281
214.55191.09870.07083.98250.36016.5939-0.1071-0.04210.2238-0.13180.01580.3952-0.1032-0.56460.09140.0427-0.0368-0.12750.10580.13470.4195-29.8846-15.8853-5.1987
220.183-0.55530.11842.140.76096.2159-0.1741-0.1231-0.04320.64360.18190.45220.1201-0.5569-0.00780.2709-0.0650.00510.37270.14780.6971-28.8552-10.616514.7647
236.0496-0.9335-0.97312.6290.06074.7064-0.0046-0.25190.8210.63870.4980.2854-0.2577-0.1065-0.49340.59780.0410.090.38550.21790.7779-26.96241.210529.9186
244.54241.56992.4652.73680.744.21910.0010.3667-0.3471-0.21090.2382-0.8708-0.19830.5326-0.23920.0925-0.085-0.03470.13020.04730.5655-7.7636-17.51820.5891
255.5351.3263-3.83781.9589-0.96555.34610.0402-0.32570.52050.83210.24460.25710.2335-0.0585-0.28480.6285-0.02-0.09430.28940.01310.4476-18.0525-14.261535.4378
263.6154-0.15721.81531.07240.78269.4384-0.39050.93460.401-0.10940.3447-0.5699-0.40421.83370.04580.4358-0.0057-0.0790.5904-0.09770.36746.1914-35.784462.8115
273.18311.1407-0.63361.28770.05110.21640.052-0.04950.11380.24340.0706-0.36940.05940.0403-0.12250.63980.1919-0.08090.47550.02220.587955.4179-40.498937.1329
285.59281.64980.14091.43121.55013.7767-0.32510.48260.2003-0.72860.7247-0.4985-0.19350.7871-0.39961.3329-0.32050.44150.8828-0.10310.601243.1633-33.952630.0162
292.46160.29222.44492.05161.74477.56320.0853-0.461-0.01490.2697-0.01960.1808-0.1692-1.0631-0.06570.16230.07870.03020.20410.03370.163825.2157-42.516255.3798
307.2243-0.1911-4.73224.53581.52984.2149-0.12470.1468-0.7377-0.8816-0.1797-0.6016-0.20050.74040.30440.68380.09750.03441.18350.01920.180237.921-47.611624.3478
310.37821.3627-0.21718.0766-2.29674.99580.0327-0.05460.54291.60550.2651.2631-0.4952-0.6073-0.29780.63430.2425-0.17660.39590.08381.1652-6.6586-35.538524.7426
328.04211.97751.42997.6476-2.11071.25210.3876-0.40580.76832.0029-0.27980.1696-0.8377-0.1986-0.10781.47780.07450.34240.8529-0.05390.626-9.2968-57.873843.0019
3312.242610.2526-7.08718.6105-5.95324.20910.11060.69750.1420.36430.35690.2365-0.242-0.6322-0.46752.24910.12320.24131.1924-0.02790.8582-11.7253-52.789950.2244
340.4319-0.50380.936912.2943-4.34754.8091-0.14030.41110.2598-2.48730.2647-1.16230.48420.5127-0.12440.6584-0.26310.08170.52380.25150.67980.7828-53.07487.1927
353.4721.2749-0.43828.5988-3.24433.2748-0.23170.19260.3021-0.06270.0525-0.84820.16310.40320.17920.1239-0.0725-0.14670.30.08150.28411.9482-54.822318.2999
368.9171.0941-4.67551.2612-0.32333.96710.12070.1480.70140.92030.30110.6036-0.1703-1.1177-0.42170.97450.33790.27030.98950.40120.5169-19.1136-69.118837.95
3700000000000000-00.3213000.321300.3213000
385.703-2.82573.32522.4367-1.89962.00010.0003-0.69370.11680.36590.08230.5655-0.089-0.3406-0.08260.3832-0.06070.12930.4525-0.01290.5429-10.369424.381253.369
391.1806-3.03251.69038.8098-4.07332.4957-0.122-0.4724-0.25780.66580.4530.8807-0.0511-0.8717-0.3310.3375-0.1889-0.05370.7619-0.06220.3017-43.490110.9186-37.5588
400.78870.19980.96882.2916-0.80261.68160.40180.3348-0.176-0.3193-0.5192-0.74590.70430.67580.11750.48560.06710.06380.56270.0580.305556.2392-51.8264-30.2649
412.67050.18020.78720.2119-1.16447.72760.04781.12420.2677-0.06730.10130.03530.31480.2216-0.14910.3207-0.07090.10640.50320.04960.385-15.9568-15.3334-16.2577
425.01721.49054.290510.806312.053114.8830.1122-1.6830.21470.4553-0.22980.02920.5094-1.17120.11760.37110.19020.02280.71-0.10720.449531.0179-33.797674.0518
432.8378-0.3704-0.79010.26791.534110.26670.02970.65230.471-0.1502-0.0095-0.1304-0.88850.0971-0.02020.3898-0.0640.02530.42010.09060.71828.7052-34.734310.2975
4437.22834.9481-19.700229.02-14.136415.10460.07420.2785-0.9343-0.2448-0.7454-0.51090.06970.18730.67120.22510.0752-0.00810.4702-0.0030.265660.460814.6226-1.7386
4510.128-2.2216-9.01990.50941.95648.06390.53050.35570.6426-0.0992-0.0654-0.2459-0.491-0.2614-0.46510.0799-0.0035-0.04940.5423-0.01940.539458.126619.0901-3.9866
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 132
2X-RAY DIFFRACTION2A135 - 218
3X-RAY DIFFRACTION3B1 - 31
4X-RAY DIFFRACTION4B32 - 218
5X-RAY DIFFRACTION5C1 - 56
6X-RAY DIFFRACTION6C57 - 218
7X-RAY DIFFRACTION7D1 - 111
8X-RAY DIFFRACTION8D112 - 217
9X-RAY DIFFRACTION9F1 - 117
10X-RAY DIFFRACTION10F118 - 218
11X-RAY DIFFRACTION11G1 - 113
12X-RAY DIFFRACTION12G114 - 217
13X-RAY DIFFRACTION13I1 - 122
14X-RAY DIFFRACTION14I123 - 218
15X-RAY DIFFRACTION15J1 - 111
16X-RAY DIFFRACTION16J112 - 218
17X-RAY DIFFRACTION17L1 - 112
18X-RAY DIFFRACTION18L113 - 220
19X-RAY DIFFRACTION19M1 - 36
20X-RAY DIFFRACTION20M37 - 218
21X-RAY DIFFRACTION21O1 - 74
22X-RAY DIFFRACTION22O75 - 178
23X-RAY DIFFRACTION23O179 - 218
24X-RAY DIFFRACTION24P1 - 112
25X-RAY DIFFRACTION25P113 - 215
26X-RAY DIFFRACTION26R2 - 114
27X-RAY DIFFRACTION27R115 - 126
28X-RAY DIFFRACTION28R127 - 218
29X-RAY DIFFRACTION29S1 - 125
30X-RAY DIFFRACTION30S126 - 218
31X-RAY DIFFRACTION31U1 - 131
32X-RAY DIFFRACTION32U132 - 196
33X-RAY DIFFRACTION33U197 - 218
34X-RAY DIFFRACTION34V1 - 36
35X-RAY DIFFRACTION35V37 - 125
36X-RAY DIFFRACTION36V126 - 218
37X-RAY DIFFRACTION37E25 - 40
38X-RAY DIFFRACTION38H12 - 23
39X-RAY DIFFRACTION39K11 - 23
40X-RAY DIFFRACTION40N11 - 23
41X-RAY DIFFRACTION41Q12 - 23
42X-RAY DIFFRACTION42T12 - 23
43X-RAY DIFFRACTION43W12 - 23
44X-RAY DIFFRACTION44X10 - 16
45X-RAY DIFFRACTION45X17 - 23

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  • 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

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