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- PDB-7cr8: Synechocystis Cas1-Cas2-prespacerL complex -

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Basic information

Entry
Database: PDB / ID: 7cr8
TitleSynechocystis Cas1-Cas2-prespacerL complex
Components
  • (DNA (36-MER)) x 2
  • CRISPR-associated endonuclease Cas1
  • CRISPR-associated endoribonuclease Cas2 1
KeywordsIMMUNE SYSTEM/DNA / CRISPR / adaptation / IMMUNE SYSTEM-DNA complex
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / RNA endonuclease activity / DNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / metal ion binding
Similarity search - Function
CRISPR-associated protein Cas1, cyanobacteria-type / CRISPR-associated endonuclease Cas2 / Virulence-associated protein D / CRISPR associated protein Cas2 / CRISPR associated protein Cas2 / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated protein Cas1 / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR associated protein Cas1
Similarity search - Domain/homology
DNA / DNA (> 10) / CRISPR-associated endoribonuclease Cas2 1 / CRISPR-associated endonuclease Cas1
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsYu, Y. / Chen, Q.
CitationJournal: Nucleic Acids Res / Year: 2021
Title: Mechanisms of spacer acquisition by sequential assembly of the adaptation module in Synechocystis.
Authors: Chengyong Wu / Dongmei Tang / Jie Cheng / Daojun Hu / Zejing Yang / Xue Ma / Haihuai He / Shaohua Yao / Tian-Min Fu / Yamei Yu / Qiang Chen /
Abstract: CRISPR-Cas immune systems process and integrate short fragments of DNA from new invaders as spacers into the host CRISPR locus to establish molecular memory of prior infection, which is also known as ...CRISPR-Cas immune systems process and integrate short fragments of DNA from new invaders as spacers into the host CRISPR locus to establish molecular memory of prior infection, which is also known as adaptation in the field. Some CRISPR-Cas systems rely on Cas1 and Cas2 to complete the adaptation process, which has been characterized in a few systems. In contrast, many other CRISPR-Cas systems require an additional factor of Cas4 for efficient adaptation, the mechanism of which remains less understood. Here we present biochemical reconstitution of the Synechocystis sp. PCC6803 type I-D adaptation system, X-ray crystal structures of Cas1-Cas2-prespacer complexes, and negative stained electron microscopy structure of the Cas4-Cas1 complex. Cas4 and Cas2 compete with each other to interact with Cas1. In the absence of prespacer, Cas4 but not Cas2 assembles with Cas1 into a very stable complex for processing the prespacer. Strikingly, the Cas1-prespacer complex develops a higher binding affinity toward Cas2 to form the Cas1-Cas2-prespacer ternary complex for integration. Together, we show a two-step sequential assembly mechanism for the type I-D adaptation module of Synechocystis, in which Cas4-Cas1 and Cas1-Cas2 function as two exclusive complexes for prespacer processing, capture, and integration.
History
DepositionAug 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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
I: CRISPR-associated endonuclease Cas1
J: CRISPR-associated endonuclease Cas1
K: CRISPR-associated endonuclease Cas1
L: CRISPR-associated endonuclease Cas1
M: CRISPR-associated endoribonuclease Cas2 1
N: CRISPR-associated endoribonuclease Cas2 1
O: DNA (36-MER)
P: DNA (36-MER)
Q: CRISPR-associated endonuclease Cas1
R: CRISPR-associated endonuclease Cas1
S: CRISPR-associated endonuclease Cas1
T: CRISPR-associated endonuclease Cas1
U: CRISPR-associated endoribonuclease Cas2 1
V: CRISPR-associated endoribonuclease Cas2 1
W: DNA (36-MER)
X: DNA (36-MER)
a: CRISPR-associated endonuclease Cas1
b: CRISPR-associated endonuclease Cas1
c: CRISPR-associated endonuclease Cas1
d: CRISPR-associated endonuclease Cas1
e: CRISPR-associated endoribonuclease Cas2 1
f: CRISPR-associated endoribonuclease Cas2 1
g: DNA (36-MER)
h: DNA (36-MER)
i: CRISPR-associated endonuclease Cas1
j: CRISPR-associated endonuclease Cas1
k: CRISPR-associated endonuclease Cas1
l: CRISPR-associated endonuclease Cas1
m: CRISPR-associated endoribonuclease Cas2 1
n: CRISPR-associated endoribonuclease Cas2 1
o: DNA (36-MER)
p: DNA (36-MER)
q: CRISPR-associated endonuclease Cas1
r: CRISPR-associated endonuclease Cas1
s: CRISPR-associated endonuclease Cas1
t: CRISPR-associated endonuclease Cas1
u: CRISPR-associated endoribonuclease Cas2 1
v: CRISPR-associated endoribonuclease Cas2 1
w: DNA (36-MER)
x: DNA (36-MER)
A: CRISPR-associated endonuclease Cas1
B: CRISPR-associated endonuclease Cas1
C: CRISPR-associated endonuclease Cas1
D: CRISPR-associated endonuclease Cas1
E: CRISPR-associated endoribonuclease Cas2 1
F: CRISPR-associated endoribonuclease Cas2 1
G: DNA (36-MER)
H: DNA (36-MER)


Theoretical massNumber of molelcules
Total (without water)1,179,72048
Polymers1,179,72048
Non-polymers00
Water0
1
I: CRISPR-associated endonuclease Cas1
J: CRISPR-associated endonuclease Cas1
K: CRISPR-associated endonuclease Cas1
L: CRISPR-associated endonuclease Cas1
M: CRISPR-associated endoribonuclease Cas2 1
N: CRISPR-associated endoribonuclease Cas2 1
O: DNA (36-MER)
P: DNA (36-MER)


Theoretical massNumber of molelcules
Total (without water)196,6208
Polymers196,6208
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21710 Å2
ΔGint-113 kcal/mol
Surface area76110 Å2
MethodPISA
2
Q: CRISPR-associated endonuclease Cas1
R: CRISPR-associated endonuclease Cas1
S: CRISPR-associated endonuclease Cas1
T: CRISPR-associated endonuclease Cas1
U: CRISPR-associated endoribonuclease Cas2 1
V: CRISPR-associated endoribonuclease Cas2 1
W: DNA (36-MER)
X: DNA (36-MER)


Theoretical massNumber of molelcules
Total (without water)196,6208
Polymers196,6208
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21730 Å2
ΔGint-115 kcal/mol
Surface area76090 Å2
MethodPISA
3
a: CRISPR-associated endonuclease Cas1
b: CRISPR-associated endonuclease Cas1
c: CRISPR-associated endonuclease Cas1
d: CRISPR-associated endonuclease Cas1
e: CRISPR-associated endoribonuclease Cas2 1
f: CRISPR-associated endoribonuclease Cas2 1
g: DNA (36-MER)
h: DNA (36-MER)


Theoretical massNumber of molelcules
Total (without water)196,6208
Polymers196,6208
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21690 Å2
ΔGint-113 kcal/mol
Surface area76250 Å2
MethodPISA
4
i: CRISPR-associated endonuclease Cas1
j: CRISPR-associated endonuclease Cas1
k: CRISPR-associated endonuclease Cas1
l: CRISPR-associated endonuclease Cas1
m: CRISPR-associated endoribonuclease Cas2 1
n: CRISPR-associated endoribonuclease Cas2 1
o: DNA (36-MER)
p: DNA (36-MER)


Theoretical massNumber of molelcules
Total (without water)196,6208
Polymers196,6208
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21590 Å2
ΔGint-111 kcal/mol
Surface area76520 Å2
MethodPISA
5
q: CRISPR-associated endonuclease Cas1
r: CRISPR-associated endonuclease Cas1
s: CRISPR-associated endonuclease Cas1
t: CRISPR-associated endonuclease Cas1
u: CRISPR-associated endoribonuclease Cas2 1
v: CRISPR-associated endoribonuclease Cas2 1
w: DNA (36-MER)
x: DNA (36-MER)


Theoretical massNumber of molelcules
Total (without water)196,6208
Polymers196,6208
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21770 Å2
ΔGint-119 kcal/mol
Surface area76260 Å2
MethodPISA
6
A: CRISPR-associated endonuclease Cas1
B: CRISPR-associated endonuclease Cas1
C: CRISPR-associated endonuclease Cas1
D: CRISPR-associated endonuclease Cas1
E: CRISPR-associated endoribonuclease Cas2 1
F: CRISPR-associated endoribonuclease Cas2 1
G: DNA (36-MER)
H: DNA (36-MER)


Theoretical massNumber of molelcules
Total (without water)196,6208
Polymers196,6208
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21730 Å2
ΔGint-111 kcal/mol
Surface area76210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.401, 185.401, 382.849
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
141
151
161
171
181
191
201
211
221
231
241
12
22
32
42
52
62
72
82
92
102
112
122
13
23
33
43
53
63
14
24
34
44
54
64

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
111SERSERLYSLYS(chain 'A' and (resid 2 through 26 or resid 30...AOA2 - 2513 - 36
121SERSERGLNGLN(chain 'A' and (resid 2 through 26 or resid 30...AOA30 - 12841 - 139
131PROPROPHEPHE(chain 'A' and (resid 2 through 26 or resid 30...AOA132 - 258143 - 269
141PHEPHELYSLYS(chain 'A' and (resid 2 through 26 or resid 30...AOA265 - 288276 - 299
151PHEPHEVALVAL(chain 'A' and (resid 2 through 26 or resid 30...AOA292 - 323303 - 334
261SERSERLYSLYS(chain 'B' and (resid 2 through 26 or resid 30...BPA2 - 2513 - 36
271SERSERGLNGLN(chain 'B' and (resid 2 through 26 or resid 30...BPA30 - 12841 - 139
281PROPROPHEPHE(chain 'B' and (resid 2 through 26 or resid 30...BPA132 - 258143 - 269
291PHEPHELYSLYS(chain 'B' and (resid 2 through 26 or resid 30...BPA265 - 288276 - 299
2101PHEPHEVALVAL(chain 'B' and (resid 2 through 26 or resid 30...BPA292 - 323303 - 334
3111SERSERLYSLYS(chain 'C' and (resid 2 through 26 or resid 30...CQA2 - 2513 - 36
3121SERSERGLNGLN(chain 'C' and (resid 2 through 26 or resid 30...CQA30 - 12841 - 139
3131PROPROPHEPHE(chain 'C' and (resid 2 through 26 or resid 30...CQA132 - 258143 - 269
3141PHEPHELYSLYS(chain 'C' and (resid 2 through 26 or resid 30...CQA265 - 288276 - 299
3151PHEPHEVALVAL(chain 'C' and (resid 2 through 26 or resid 30...CQA292 - 323303 - 334
4161SERSERLYSLYS(chain 'D' and (resid 2 through 26 or resid 30...DRA2 - 2513 - 36
4171SERSERGLNGLN(chain 'D' and (resid 2 through 26 or resid 30...DRA30 - 12841 - 139
4181PROPROPHEPHE(chain 'D' and (resid 2 through 26 or resid 30...DRA132 - 258143 - 269
4191PHEPHELYSLYS(chain 'D' and (resid 2 through 26 or resid 30...DRA265 - 288276 - 299
4201PHEPHEVALVAL(chain 'D' and (resid 2 through 26 or resid 30...DRA292 - 323303 - 334
5211SERSERLYSLYS(chain 'I' and (resid 2 through 26 or resid 30...IA2 - 2513 - 36
5221SERSERGLNGLN(chain 'I' and (resid 2 through 26 or resid 30...IA30 - 12841 - 139
5231PROPROPHEPHE(chain 'I' and (resid 2 through 26 or resid 30...IA132 - 258143 - 269
5241PHEPHELYSLYS(chain 'I' and (resid 2 through 26 or resid 30...IA265 - 288276 - 299
5251PHEPHEVALVAL(chain 'I' and (resid 2 through 26 or resid 30...IA292 - 323303 - 334
6261SERSERLYSLYS(chain 'J' and (resid 2 through 26 or resid 30...JB2 - 2513 - 36
6271SERSERGLNGLN(chain 'J' and (resid 2 through 26 or resid 30...JB30 - 12841 - 139
6281PROPROPHEPHE(chain 'J' and (resid 2 through 26 or resid 30...JB132 - 258143 - 269
6291PHEPHELYSLYS(chain 'J' and (resid 2 through 26 or resid 30...JB265 - 288276 - 299
6301PHEPHEVALVAL(chain 'J' and (resid 2 through 26 or resid 30...JB292 - 323303 - 334
7311SERSERLYSLYS(chain 'K' and (resid 2 through 26 or resid 30...KC2 - 2513 - 36
7321SERSERGLNGLN(chain 'K' and (resid 2 through 26 or resid 30...KC30 - 12841 - 139
7331PROPROPHEPHE(chain 'K' and (resid 2 through 26 or resid 30...KC132 - 258143 - 269
7341PHEPHELYSLYS(chain 'K' and (resid 2 through 26 or resid 30...KC265 - 288276 - 299
7351PHEPHEVALVAL(chain 'K' and (resid 2 through 26 or resid 30...KC292 - 323303 - 334
8361SERSERLYSLYS(chain 'L' and (resid 2 through 26 or resid 30...LD2 - 2513 - 36
8371SERSERGLNGLN(chain 'L' and (resid 2 through 26 or resid 30...LD30 - 12841 - 139
8381PROPROPHEPHE(chain 'L' and (resid 2 through 26 or resid 30...LD132 - 258143 - 269
8391PHEPHELYSLYS(chain 'L' and (resid 2 through 26 or resid 30...LD265 - 288276 - 299
8401PHEPHEVALVAL(chain 'L' and (resid 2 through 26 or resid 30...LD292 - 323303 - 334
9411SERSERLYSLYS(chain 'Q' and (resid 2 through 26 or resid 30...QI2 - 2513 - 36
9421SERSERGLNGLN(chain 'Q' and (resid 2 through 26 or resid 30...QI30 - 12841 - 139
9431PROPROPHEPHE(chain 'Q' and (resid 2 through 26 or resid 30...QI132 - 258143 - 269
9441PHEPHELYSLYS(chain 'Q' and (resid 2 through 26 or resid 30...QI265 - 288276 - 299
9451PHEPHEVALVAL(chain 'Q' and (resid 2 through 26 or resid 30...QI292 - 323303 - 334
10461SERSERLYSLYS(chain 'R' and (resid 2 through 26 or resid 30...RJ2 - 2513 - 36
10471SERSERGLNGLN(chain 'R' and (resid 2 through 26 or resid 30...RJ30 - 12841 - 139
10481PROPROPHEPHE(chain 'R' and (resid 2 through 26 or resid 30...RJ132 - 258143 - 269
10491PHEPHELYSLYS(chain 'R' and (resid 2 through 26 or resid 30...RJ265 - 288276 - 299
10501PHEPHEVALVAL(chain 'R' and (resid 2 through 26 or resid 30...RJ292 - 323303 - 334
11511SERSERLYSLYS(chain 'S' and (resid 2 through 26 or resid 30...SK2 - 2513 - 36
11521SERSERGLNGLN(chain 'S' and (resid 2 through 26 or resid 30...SK30 - 12841 - 139
11531PROPROPHEPHE(chain 'S' and (resid 2 through 26 or resid 30...SK132 - 258143 - 269
11541PHEPHELYSLYS(chain 'S' and (resid 2 through 26 or resid 30...SK265 - 288276 - 299
11551PHEPHEVALVAL(chain 'S' and (resid 2 through 26 or resid 30...SK292 - 323303 - 334
12561SERSERLYSLYS(chain 'T' and (resid 2 through 26 or resid 30...TL2 - 2513 - 36
12571SERSERGLNGLN(chain 'T' and (resid 2 through 26 or resid 30...TL30 - 12841 - 139
12581PROPROPHEPHE(chain 'T' and (resid 2 through 26 or resid 30...TL132 - 258143 - 269
12591PHEPHELYSLYS(chain 'T' and (resid 2 through 26 or resid 30...TL265 - 288276 - 299
12601PHEPHEVALVAL(chain 'T' and (resid 2 through 26 or resid 30...TL292 - 323303 - 334
13611SERSERLYSLYS(chain 'a' and (resid 2 through 26 or resid 30...aQ2 - 2513 - 36
13621SERSERGLNGLN(chain 'a' and (resid 2 through 26 or resid 30...aQ30 - 12841 - 139
13631PROPROPHEPHE(chain 'a' and (resid 2 through 26 or resid 30...aQ132 - 258143 - 269
13641PHEPHELYSLYS(chain 'a' and (resid 2 through 26 or resid 30...aQ265 - 288276 - 299
13651PHEPHEVALVAL(chain 'a' and (resid 2 through 26 or resid 30...aQ292 - 323303 - 334
14661SERSERLYSLYS(chain 'b' and (resid 2 through 26 or resid 30...bR2 - 2513 - 36
14671SERSERGLNGLN(chain 'b' and (resid 2 through 26 or resid 30...bR30 - 12841 - 139
14681PROPROPHEPHE(chain 'b' and (resid 2 through 26 or resid 30...bR132 - 258143 - 269
14691PHEPHELYSLYS(chain 'b' and (resid 2 through 26 or resid 30...bR265 - 288276 - 299
14701PHEPHEVALVAL(chain 'b' and (resid 2 through 26 or resid 30...bR292 - 323303 - 334
15711SERSERLYSLYS(chain 'c' and (resid 2 through 26 or resid 30...cS2 - 2513 - 36
15721SERSERGLNGLN(chain 'c' and (resid 2 through 26 or resid 30...cS30 - 12841 - 139
15731PROPROPHEPHE(chain 'c' and (resid 2 through 26 or resid 30...cS132 - 258143 - 269
15741PHEPHELYSLYS(chain 'c' and (resid 2 through 26 or resid 30...cS265 - 288276 - 299
15751PHEPHEVALVAL(chain 'c' and (resid 2 through 26 or resid 30...cS292 - 323303 - 334
16761SERSERLYSLYS(chain 'd' and (resid 2 through 26 or resid 30...dT2 - 2513 - 36
16771SERSERGLNGLN(chain 'd' and (resid 2 through 26 or resid 30...dT30 - 12841 - 139
16781PROPROPHEPHE(chain 'd' and (resid 2 through 26 or resid 30...dT132 - 258143 - 269
16791PHEPHELYSLYS(chain 'd' and (resid 2 through 26 or resid 30...dT265 - 288276 - 299
16801PHEPHEVALVAL(chain 'd' and (resid 2 through 26 or resid 30...dT292 - 323303 - 334
17811SERSERLYSLYS(chain 'i' and (resid 2 through 26 or resid 30...iY2 - 2513 - 36
17821SERSERGLNGLN(chain 'i' and (resid 2 through 26 or resid 30...iY30 - 12841 - 139
17831PROPROPHEPHE(chain 'i' and (resid 2 through 26 or resid 30...iY132 - 258143 - 269
17841PHEPHELYSLYS(chain 'i' and (resid 2 through 26 or resid 30...iY265 - 288276 - 299
17851PHEPHEVALVAL(chain 'i' and (resid 2 through 26 or resid 30...iY292 - 323303 - 334
18861SERSERLYSLYS(chain 'j' and (resid 2 through 26 or resid 30...jZ2 - 2513 - 36
18871SERSERGLNGLN(chain 'j' and (resid 2 through 26 or resid 30...jZ30 - 12841 - 139
18881PROPROPHEPHE(chain 'j' and (resid 2 through 26 or resid 30...jZ132 - 258143 - 269
18891PHEPHELYSLYS(chain 'j' and (resid 2 through 26 or resid 30...jZ265 - 288276 - 299
18901PHEPHEVALVAL(chain 'j' and (resid 2 through 26 or resid 30...jZ292 - 323303 - 334
19911SERSERLYSLYS(chain 'k' and (resid 2 through 26 or resid 30...kAA2 - 2513 - 36
19921SERSERGLNGLN(chain 'k' and (resid 2 through 26 or resid 30...kAA30 - 12841 - 139
19931PROPROPHEPHE(chain 'k' and (resid 2 through 26 or resid 30...kAA132 - 258143 - 269
19941PHEPHELYSLYS(chain 'k' and (resid 2 through 26 or resid 30...kAA265 - 288276 - 299
19951PHEPHEVALVAL(chain 'k' and (resid 2 through 26 or resid 30...kAA292 - 323303 - 334
20961SERSERLYSLYS(chain 'l' and (resid 2 through 26 or resid 30...lBA2 - 2513 - 36
20971SERSERGLNGLN(chain 'l' and (resid 2 through 26 or resid 30...lBA30 - 12841 - 139
20981PROPROPHEPHE(chain 'l' and (resid 2 through 26 or resid 30...lBA132 - 258143 - 269
20991PHEPHELYSLYS(chain 'l' and (resid 2 through 26 or resid 30...lBA265 - 288276 - 299
201001PHEPHEVALVAL(chain 'l' and (resid 2 through 26 or resid 30...lBA292 - 323303 - 334
211011SERSERLYSLYS(chain 'q' and (resid 2 through 26 or resid 30...qGA2 - 2513 - 36
211021SERSERGLNGLN(chain 'q' and (resid 2 through 26 or resid 30...qGA30 - 12841 - 139
211031PROPROPHEPHE(chain 'q' and (resid 2 through 26 or resid 30...qGA132 - 258143 - 269
211041PHEPHELYSLYS(chain 'q' and (resid 2 through 26 or resid 30...qGA265 - 288276 - 299
211051PHEPHEVALVAL(chain 'q' and (resid 2 through 26 or resid 30...qGA292 - 323303 - 334
221061SERSERLYSLYS(chain 'r' and (resid 2 through 26 or resid 30...rHA2 - 2513 - 36
221071SERSERGLNGLN(chain 'r' and (resid 2 through 26 or resid 30...rHA30 - 12841 - 139
221081PROPROPHEPHE(chain 'r' and (resid 2 through 26 or resid 30...rHA132 - 258143 - 269
221091PHEPHELYSLYS(chain 'r' and (resid 2 through 26 or resid 30...rHA265 - 288276 - 299
221101PHEPHEVALVAL(chain 'r' and (resid 2 through 26 or resid 30...rHA292 - 323303 - 334
231111SERSERLYSLYS(chain 's' and (resid 2 through 26 or resid 30...sIA2 - 2513 - 36
231121SERSERGLNGLN(chain 's' and (resid 2 through 26 or resid 30...sIA30 - 12841 - 139
231131PROPROPHEPHE(chain 's' and (resid 2 through 26 or resid 30...sIA132 - 258143 - 269
231141PHEPHELYSLYS(chain 's' and (resid 2 through 26 or resid 30...sIA265 - 288276 - 299
231151PHEPHEVALVAL(chain 's' and (resid 2 through 26 or resid 30...sIA292 - 323303 - 334
241161SERSERLYSLYS(chain 't' and (resid 2 through 26 or resid 30...tJA2 - 2513 - 36
241171SERSERGLNGLN(chain 't' and (resid 2 through 26 or resid 30...tJA30 - 12841 - 139
241181PROPROPHEPHE(chain 't' and (resid 2 through 26 or resid 30...tJA132 - 258143 - 269
241191PHEPHELYSLYS(chain 't' and (resid 2 through 26 or resid 30...tJA265 - 288276 - 299
241201PHEPHEVALVAL(chain 't' and (resid 2 through 26 or resid 30...tJA292 - 323303 - 334
11212LEULEUILEILE(chain 'E' and resid 2 through 93)ESA2 - 9213 - 103
21222LEULEUILEILE(chain 'F' and resid 2 through 93)FTA2 - 9213 - 103
31232LEULEUILEILE(chain 'M' and resid 2 through 93)ME2 - 9213 - 103
41242LEULEUILEILE(chain 'N' and resid 2 through 93)NF2 - 9213 - 103
51252LEULEUILEILE(chain 'U' and resid 2 through 93)UM2 - 9213 - 103
61262LEULEUILEILE(chain 'V' and resid 2 through 93)VN2 - 9213 - 103
71272LEULEUILEILE(chain 'e' and resid 2 through 93)eU2 - 9213 - 103
81282LEULEUILEILE(chain 'f' and resid 2 through 93)fV2 - 9213 - 103
91292LEULEUILEILE(chain 'm' and resid 2 through 93)mCA2 - 9213 - 103
101302LEULEUILEILE(chain 'n' and resid 2 through 93)nDA2 - 9213 - 103
111312LEULEUILEILE(chain 'u' and resid 2 through 93)uKA2 - 9213 - 103
121322LEULEUILEILE(chain 'v' and resid 2 through 93)vLA2 - 9213 - 103
11333DTDTDCDC(chain 'G' and (resid 6 through 28 or resid 31 through 33))GUA6 - 286 - 28
11343DGDGDTDT(chain 'G' and (resid 6 through 28 or resid 31 through 33))GUA31 - 3331 - 33
21353DTDTDCDC(chain 'O' and (resid 6 through 28 or resid 31 through 33))OG6 - 286 - 28
21363DGDGDTDT(chain 'O' and (resid 6 through 28 or resid 31 through 33))OG31 - 3331 - 33
31373DTDTDCDC(chain 'W' and (resid 6 through 28 or resid 31 through 33))WO6 - 286 - 28
31383DGDGDTDT(chain 'W' and (resid 6 through 28 or resid 31 through 33))WO31 - 3331 - 33
41393DTDTDCDC(chain 'g' and (resid 6 through 28 or resid 31 through 33))gW6 - 286 - 28
41403DGDGDTDT(chain 'g' and (resid 6 through 28 or resid 31 through 33))gW31 - 3331 - 33
51413DTDTDCDC(chain 'o' and (resid 6 through 28 or resid 31 through 33))oEA6 - 286 - 28
51423DGDGDTDT(chain 'o' and (resid 6 through 28 or resid 31 through 33))oEA31 - 3331 - 33
61433DTDTDCDC(chain 'w' and (resid 6 through 28 or resid 31 through 33))wMA6 - 286 - 28
61443DGDGDTDT(chain 'w' and (resid 6 through 28 or resid 31 through 33))wMA31 - 3331 - 33
11454DTDTDCDC(chain 'H' and (resid 8 through 29 or resid 32 through 34))HVA8 - 298 - 29
11464DTDTDTDT(chain 'H' and (resid 8 through 29 or resid 32 through 34))HVA32 - 3432 - 34
21474DTDTDCDC(chain 'P' and (resid 8 through 29 or resid 32 through 34))PH8 - 298 - 29
21484DTDTDTDT(chain 'P' and (resid 8 through 29 or resid 32 through 34))PH32 - 3432 - 34
31494DTDTDCDC(chain 'X' and (resid 8 through 29 or resid 32 through 34))XP8 - 298 - 29
31504DTDTDTDT(chain 'X' and (resid 8 through 29 or resid 32 through 34))XP32 - 3432 - 34
41514DTDTDCDC(chain 'h' and (resid 8 through 29 or resid 32 through 34))hX8 - 298 - 29
41524DTDTDTDT(chain 'h' and (resid 8 through 29 or resid 32 through 34))hX32 - 3432 - 34
51534DTDTDCDC(chain 'p' and (resid 8 through 29 or resid 32 through 34))pFA8 - 298 - 29
51544DTDTDTDT(chain 'p' and (resid 8 through 29 or resid 32 through 34))pFA32 - 3432 - 34
61554DTDTDCDC(chain 'x' and (resid 8 through 29 or resid 32 through 34))xNA8 - 298 - 29
61564DTDTDTDT(chain 'x' and (resid 8 through 29 or resid 32 through 34))xNA32 - 3432 - 34

NCS ensembles :
ID
1
2
3
4

-
Components

#1: Protein ...
CRISPR-associated endonuclease Cas1


Mass: 37811.238 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: cas1, slr7016 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6ZEI2, Hydrolases; Acting on ester bonds
#2: Protein
CRISPR-associated endoribonuclease Cas2 1


Mass: 11656.425 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: cas2-1, ssr7017 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6ZEI1, Hydrolases; Acting on ester bonds
#3: DNA chain
DNA (36-MER)


Mass: 11004.026 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain
DNA (36-MER)


Mass: 11058.110 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Experimental details

-
Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% MPD, 0.1 M imidazole pH 6.5, 0.2 M (NH4)2SO4, 10% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.69→50 Å / Num. obs: 157305 / % possible obs: 99.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 130.45 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.68
Reflection shellResolution: 3.69→3.92 Å / Num. unique obs: 25305 / CC1/2: 0.838

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CR6

7cr6


Resolution: 3.7→47.56 Å / SU ML: 0.7752 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 42.3464
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3409 1566 1 %
Rwork0.2955 155399 -
obs0.2959 156965 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 147.92 Å2
Refinement stepCycle: LAST / Resolution: 3.7→47.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms71378 7242 0 0 78620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004181050
X-RAY DIFFRACTIONf_angle_d0.9485111106
X-RAY DIFFRACTIONf_chiral_restr0.043412313
X-RAY DIFFRACTIONf_plane_restr0.005913021
X-RAY DIFFRACTIONf_dihedral_angle_d10.865947316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.820.46921420.394914089X-RAY DIFFRACTION99.65
3.82-3.950.49261430.375414153X-RAY DIFFRACTION99.71
3.95-4.110.36861420.348714093X-RAY DIFFRACTION99.84
4.11-4.30.36151420.340414211X-RAY DIFFRACTION99.89
4.3-4.520.36121430.310414156X-RAY DIFFRACTION99.88
4.52-4.810.331410.296414064X-RAY DIFFRACTION99.96
4.81-5.180.36461440.30714187X-RAY DIFFRACTION99.92
5.18-5.70.40891420.320514118X-RAY DIFFRACTION99.99
5.7-6.520.34821430.33214150X-RAY DIFFRACTION99.97
6.52-8.210.37541430.296314173X-RAY DIFFRACTION99.94
8.21-47.560.23011410.214714005X-RAY DIFFRACTION98.85

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