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- PDB-6fiz: Crystal Structure of CNG mimicking NaK-EAPP mutant (T67A) cocryst... -

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Basic information

Entry
Database: PDB / ID: 6fiz
TitleCrystal Structure of CNG mimicking NaK-EAPP mutant (T67A) cocrystallized with K+
ComponentsPotassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
KeywordsTRANSPORT PROTEIN / CNG mimick / ion channel / transport channel
Function / homology
Function and homology information


response to stimulus / VxPx cargo-targeting to cilium / intracellularly cGMP-activated cation channel activity / Golgi-associated vesicle membrane / intracellularly cAMP-activated cation channel activity / ciliary membrane / potassium channel activity / cGMP binding / cAMP binding / sensory perception of smell ...response to stimulus / VxPx cargo-targeting to cilium / intracellularly cGMP-activated cation channel activity / Golgi-associated vesicle membrane / intracellularly cAMP-activated cation channel activity / ciliary membrane / potassium channel activity / cGMP binding / cAMP binding / sensory perception of smell / membrane => GO:0016020 / calmodulin binding / Golgi membrane / identical protein binding / membrane / metal ion binding
Similarity search - Function
Cyclic nucleotide-gated channel, C-terminal leucine zipper domain / C-terminal leucine zipper domain of cyclic nucleotide-gated channels / Two pore domain potassium channel / Cyclic nucleotide-binding domain signature 2. / Helix Hairpins - #70 / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Potassium channel domain / Ion channel / Cyclic nucleotide-monophosphate binding domain ...Cyclic nucleotide-gated channel, C-terminal leucine zipper domain / C-terminal leucine zipper domain of cyclic nucleotide-gated channels / Two pore domain potassium channel / Cyclic nucleotide-binding domain signature 2. / Helix Hairpins - #70 / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Potassium channel domain / Ion channel / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Ion transport domain / Ion transport protein / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
GLYCINE / : / Cyclic nucleotide-gated olfactory channel / Potassium channel protein
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsNapolitano, L.M.R. / De March, M. / Steiner, R.A. / Onesti, S.
CitationJournal: To Be Published
Title: Crystal Structure of CNG mimicking NaK-EAPP mutant (T67A) cocrystallized with K+
Authors: Napolitano, L.M.R. / De March, M. / Onesti, S. / Steiner, R.A.
History
DepositionJan 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2Jun 26, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _audit_author.name / _citation_author.name / _entity.pdbx_description
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
B: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
C: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
D: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
E: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
F: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
G: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
H: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
I: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
J: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
K: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
L: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
M: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
N: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
O: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
P: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,50695
Polymers164,70616
Non-polymers5,80079
Water1,71195
1
A: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
B: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
C: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
D: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,16318
Polymers41,1764
Non-polymers98614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-71 kcal/mol
Surface area17600 Å2
MethodPISA
2
E: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
F: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
G: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
H: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,43121
Polymers41,1764
Non-polymers1,25417
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-85 kcal/mol
Surface area17300 Å2
MethodPISA
3
I: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
J: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
K: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
L: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,80626
Polymers41,1764
Non-polymers1,63022
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-90 kcal/mol
Surface area17430 Å2
MethodPISA
4
M: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
N: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
O: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
P: Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,10730
Polymers41,1764
Non-polymers1,93026
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7940 Å2
ΔGint-89 kcal/mol
Surface area17590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.220, 135.250, 67.430
Angle α, β, γ (deg.)90.00, 91.95, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18A
28I
19A
29J
110A
210K
111A
211L
112A
212M
113A
213N
114A
214O
115A
215P
116B
216C
117B
217D
118B
218E
119B
219F
120B
220G
121B
221H
122B
222I
123B
223J
124B
224K
125B
225L
126B
226M
127B
227N
128B
228O
129B
229P
130C
230D
131C
231E
132C
232F
133C
233G
134C
234H
135C
235I
136C
236J
137C
237K
138C
238L
139C
239M
140C
240N
141C
241O
142C
242P
143D
243E
144D
244F
145D
245G
146D
246H
147D
247I
148D
248J
149D
249K
150D
250L
151D
251M
152D
252N
153D
253O
154D
254P
155E
255F
156E
256G
157E
257H
158E
258I
159E
259J
160E
260K
161E
261L
162E
262M
163E
263N
164E
264O
165E
265P
166F
266G
167F
267H
168F
268I
169F
269J
170F
270K
171F
271L
172F
272M
173F
273N
174F
274O
175F
275P
176G
276H
177G
277I
178G
278J
179G
279K
180G
280L
181G
281M
182G
282N
183G
283O
184G
284P
185H
285I
186H
286J
187H
287K
188H
288L
189H
289M
190H
290N
191H
291O
192H
292P
193I
293J
194I
294K
195I
295L
196I
296M
197I
297N
198I
298O
199I
299P
1100J
2100K
1101J
2101L
1102J
2102M
1103J
2103N
1104J
2104O
1105J
2105P
1106K
2106L
1107K
2107M
1108K
2108N
1109K
2109O
1110K
2110P
1111L
2111M
1112L
2112N
1113L
2113O
1114L
2114P
1115M
2115N
1116M
2116O
1117M
2117P
1118N
2118O
1119N
2119P
1120O
2120P

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
11LYSLYSPROPROAA22 - 1124 - 94
21LYSLYSPROPROBB22 - 1124 - 94
12LYSLYSPROPROAA22 - 1124 - 94
22LYSLYSPROPROCC22 - 1124 - 94
13LYSLYSPROPROAA22 - 1124 - 94
23LYSLYSPROPRODD22 - 1124 - 94
14LYSLYSPROPROAA22 - 1124 - 94
24LYSLYSPROPROEE22 - 1124 - 94
15LYSLYSPROPROAA22 - 1124 - 94
25LYSLYSPROPROFF22 - 1124 - 94
16LYSLYSPROPROAA22 - 1124 - 94
26LYSLYSPROPROGG22 - 1124 - 94
17LYSLYSPROPROAA22 - 1124 - 94
27LYSLYSPROPROHH22 - 1124 - 94
18LYSLYSVALVALAA22 - 1114 - 93
28LYSLYSVALVALII22 - 1114 - 93
19LYSLYSPROPROAA22 - 1124 - 94
29LYSLYSPROPROJJ22 - 1124 - 94
110LYSLYSPROPROAA22 - 1124 - 94
210LYSLYSPROPROKK22 - 1124 - 94
111LYSLYSPROPROAA22 - 1124 - 94
211LYSLYSPROPROLL22 - 1124 - 94
112LYSLYSVALVALAA22 - 1114 - 93
212LYSLYSVALVALMM22 - 1114 - 93
113LYSLYSPROPROAA22 - 1124 - 94
213LYSLYSPROPRONN22 - 1124 - 94
114LYSLYSPROPROAA22 - 1124 - 94
214LYSLYSPROPROOO22 - 1124 - 94
115LYSLYSPROPROAA22 - 1124 - 94
215LYSLYSPROPROPP22 - 1124 - 94
116LYSLYSPROPROBB22 - 1124 - 94
216LYSLYSPROPROCC22 - 1124 - 94
117LYSLYSPROPROBB22 - 1124 - 94
217LYSLYSPROPRODD22 - 1124 - 94
118LYSLYSPROPROBB22 - 1124 - 94
218LYSLYSPROPROEE22 - 1124 - 94
119LYSLYSPROPROBB22 - 1124 - 94
219LYSLYSPROPROFF22 - 1124 - 94
120LYSLYSPROPROBB22 - 1124 - 94
220LYSLYSPROPROGG22 - 1124 - 94
121LYSLYSPROPROBB22 - 1124 - 94
221LYSLYSPROPROHH22 - 1124 - 94
122LYSLYSVALVALBB22 - 1114 - 93
222LYSLYSVALVALII22 - 1114 - 93
123LYSLYSPROPROBB22 - 1124 - 94
223LYSLYSPROPROJJ22 - 1124 - 94
124LYSLYSPROPROBB22 - 1124 - 94
224LYSLYSPROPROKK22 - 1124 - 94
125LYSLYSPROPROBB22 - 1124 - 94
225LYSLYSPROPROLL22 - 1124 - 94
126LYSLYSVALVALBB22 - 1114 - 93
226LYSLYSVALVALMM22 - 1114 - 93
127LYSLYSPROPROBB22 - 1124 - 94
227LYSLYSPROPRONN22 - 1124 - 94
128LYSLYSPROPROBB22 - 1124 - 94
228LYSLYSPROPROOO22 - 1124 - 94
129LYSLYSPROPROBB22 - 1124 - 94
229LYSLYSPROPROPP22 - 1124 - 94
130LYSLYSPROPROCC22 - 1124 - 94
230LYSLYSPROPRODD22 - 1124 - 94
131LYSLYSPROPROCC22 - 1124 - 94
231LYSLYSPROPROEE22 - 1124 - 94
132LYSLYSPROPROCC22 - 1124 - 94
232LYSLYSPROPROFF22 - 1124 - 94
133LYSLYSPROPROCC22 - 1124 - 94
233LYSLYSPROPROGG22 - 1124 - 94
134LYSLYSPROPROCC22 - 1124 - 94
234LYSLYSPROPROHH22 - 1124 - 94
135LYSLYSVALVALCC22 - 1114 - 93
235LYSLYSVALVALII22 - 1114 - 93
136LYSLYSPROPROCC22 - 1124 - 94
236LYSLYSPROPROJJ22 - 1124 - 94
137LYSLYSPROPROCC22 - 1124 - 94
237LYSLYSPROPROKK22 - 1124 - 94
138LYSLYSPROPROCC22 - 1124 - 94
238LYSLYSPROPROLL22 - 1124 - 94
139LYSLYSVALVALCC22 - 1114 - 93
239LYSLYSVALVALMM22 - 1114 - 93
140LYSLYSPROPROCC22 - 1124 - 94
240LYSLYSPROPRONN22 - 1124 - 94
141LYSLYSPROPROCC22 - 1124 - 94
241LYSLYSPROPROOO22 - 1124 - 94
142LYSLYSPROPROCC22 - 1124 - 94
242LYSLYSPROPROPP22 - 1124 - 94
143LYSLYSPROPRODD22 - 1124 - 94
243LYSLYSPROPROEE22 - 1124 - 94
144LYSLYSPROPRODD22 - 1124 - 94
244LYSLYSPROPROFF22 - 1124 - 94
145LYSLYSPROPRODD22 - 1124 - 94
245LYSLYSPROPROGG22 - 1124 - 94
146LYSLYSPROPRODD22 - 1124 - 94
246LYSLYSPROPROHH22 - 1124 - 94
147LYSLYSVALVALDD22 - 1114 - 93
247LYSLYSVALVALII22 - 1114 - 93
148LYSLYSPROPRODD22 - 1124 - 94
248LYSLYSPROPROJJ22 - 1124 - 94
149LYSLYSPROPRODD22 - 1124 - 94
249LYSLYSPROPROKK22 - 1124 - 94
150LYSLYSPROPRODD22 - 1124 - 94
250LYSLYSPROPROLL22 - 1124 - 94
151LYSLYSVALVALDD22 - 1114 - 93
251LYSLYSVALVALMM22 - 1114 - 93
152LYSLYSPROPRODD22 - 1124 - 94
252LYSLYSPROPRONN22 - 1124 - 94
153LYSLYSPROPRODD22 - 1124 - 94
253LYSLYSPROPROOO22 - 1124 - 94
154LYSLYSPROPRODD22 - 1124 - 94
254LYSLYSPROPROPP22 - 1124 - 94
155LYSLYSPROPROEE22 - 1124 - 94
255LYSLYSPROPROFF22 - 1124 - 94
156LYSLYSPROPROEE22 - 1124 - 94
256LYSLYSPROPROGG22 - 1124 - 94
157LYSLYSPROPROEE22 - 1124 - 94
257LYSLYSPROPROHH22 - 1124 - 94
158LYSLYSVALVALEE22 - 1114 - 93
258LYSLYSVALVALII22 - 1114 - 93
159LYSLYSPROPROEE22 - 1124 - 94
259LYSLYSPROPROJJ22 - 1124 - 94
160LYSLYSPROPROEE22 - 1124 - 94
260LYSLYSPROPROKK22 - 1124 - 94
161LYSLYSPROPROEE22 - 1124 - 94
261LYSLYSPROPROLL22 - 1124 - 94
162LYSLYSVALVALEE22 - 1114 - 93
262LYSLYSVALVALMM22 - 1114 - 93
163LYSLYSPROPROEE22 - 1124 - 94
263LYSLYSPROPRONN22 - 1124 - 94
164LYSLYSPROPROEE22 - 1124 - 94
264LYSLYSPROPROOO22 - 1124 - 94
165LYSLYSPROPROEE22 - 1124 - 94
265LYSLYSPROPROPP22 - 1124 - 94
166LYSLYSPROPROFF22 - 1124 - 94
266LYSLYSPROPROGG22 - 1124 - 94
167LYSLYSPROPROFF22 - 1124 - 94
267LYSLYSPROPROHH22 - 1124 - 94
168LYSLYSVALVALFF22 - 1114 - 93
268LYSLYSVALVALII22 - 1114 - 93
169LYSLYSPROPROFF22 - 1124 - 94
269LYSLYSPROPROJJ22 - 1124 - 94
170LYSLYSPROPROFF22 - 1124 - 94
270LYSLYSPROPROKK22 - 1124 - 94
171LYSLYSPROPROFF22 - 1124 - 94
271LYSLYSPROPROLL22 - 1124 - 94
172LYSLYSVALVALFF22 - 1114 - 93
272LYSLYSVALVALMM22 - 1114 - 93
173LYSLYSPROPROFF22 - 1124 - 94
273LYSLYSPROPRONN22 - 1124 - 94
174LYSLYSPROPROFF22 - 1124 - 94
274LYSLYSPROPROOO22 - 1124 - 94
175LYSLYSPROPROFF22 - 1124 - 94
275LYSLYSPROPROPP22 - 1124 - 94
176LYSLYSPROPROGG22 - 1124 - 94
276LYSLYSPROPROHH22 - 1124 - 94
177LYSLYSVALVALGG22 - 1114 - 93
277LYSLYSVALVALII22 - 1114 - 93
178LYSLYSPROPROGG22 - 1124 - 94
278LYSLYSPROPROJJ22 - 1124 - 94
179LYSLYSPROPROGG22 - 1124 - 94
279LYSLYSPROPROKK22 - 1124 - 94
180LYSLYSPROPROGG22 - 1124 - 94
280LYSLYSPROPROLL22 - 1124 - 94
181LYSLYSVALVALGG22 - 1114 - 93
281LYSLYSVALVALMM22 - 1114 - 93
182LYSLYSPROPROGG22 - 1124 - 94
282LYSLYSPROPRONN22 - 1124 - 94
183LYSLYSPROPROGG22 - 1124 - 94
283LYSLYSPROPROOO22 - 1124 - 94
184LYSLYSPROPROGG22 - 1124 - 94
284LYSLYSPROPROPP22 - 1124 - 94
185LYSLYSVALVALHH22 - 1114 - 93
285LYSLYSVALVALII22 - 1114 - 93
186LYSLYSPROPROHH22 - 1124 - 94
286LYSLYSPROPROJJ22 - 1124 - 94
187LYSLYSPROPROHH22 - 1124 - 94
287LYSLYSPROPROKK22 - 1124 - 94
188LYSLYSPROPROHH22 - 1124 - 94
288LYSLYSPROPROLL22 - 1124 - 94
189LYSLYSVALVALHH22 - 1114 - 93
289LYSLYSVALVALMM22 - 1114 - 93
190LYSLYSPROPROHH22 - 1124 - 94
290LYSLYSPROPRONN22 - 1124 - 94
191LYSLYSPROPROHH22 - 1124 - 94
291LYSLYSPROPROOO22 - 1124 - 94
192LYSLYSPROPROHH22 - 1124 - 94
292LYSLYSPROPROPP22 - 1124 - 94
193LYSLYSVALVALII22 - 1114 - 93
293LYSLYSVALVALJJ22 - 1114 - 93
194LYSLYSVALVALII22 - 1114 - 93
294LYSLYSVALVALKK22 - 1114 - 93
195LYSLYSVALVALII22 - 1114 - 93
295LYSLYSVALVALLL22 - 1114 - 93
196ALAALAPROPROII19 - 1121 - 94
296ALAALAPROPROMM19 - 1121 - 94
197LYSLYSVALVALII22 - 1114 - 93
297LYSLYSVALVALNN22 - 1114 - 93
198LYSLYSVALVALII22 - 1114 - 93
298LYSLYSVALVALOO22 - 1114 - 93
199LYSLYSVALVALII22 - 1114 - 93
299LYSLYSVALVALPP22 - 1114 - 93
1100LYSLYSPROPROJJ22 - 1124 - 94
2100LYSLYSPROPROKK22 - 1124 - 94
1101LYSLYSPROPROJJ22 - 1124 - 94
2101LYSLYSPROPROLL22 - 1124 - 94
1102LYSLYSVALVALJJ22 - 1114 - 93
2102LYSLYSVALVALMM22 - 1114 - 93
1103LYSLYSPROPROJJ22 - 1124 - 94
2103LYSLYSPROPRONN22 - 1124 - 94
1104LYSLYSPROPROJJ22 - 1124 - 94
2104LYSLYSPROPROOO22 - 1124 - 94
1105LYSLYSPROPROJJ22 - 1124 - 94
2105LYSLYSPROPROPP22 - 1124 - 94
1106LYSLYSPROPROKK22 - 1124 - 94
2106LYSLYSPROPROLL22 - 1124 - 94
1107LYSLYSVALVALKK22 - 1114 - 93
2107LYSLYSVALVALMM22 - 1114 - 93
1108LYSLYSPROPROKK22 - 1124 - 94
2108LYSLYSPROPRONN22 - 1124 - 94
1109LYSLYSPROPROKK22 - 1124 - 94
2109LYSLYSPROPROOO22 - 1124 - 94
1110LYSLYSPROPROKK22 - 1124 - 94
2110LYSLYSPROPROPP22 - 1124 - 94
1111LYSLYSVALVALLL22 - 1114 - 93
2111LYSLYSVALVALMM22 - 1114 - 93
1112LYSLYSPROPROLL22 - 1124 - 94
2112LYSLYSPROPRONN22 - 1124 - 94
1113LYSLYSPROPROLL22 - 1124 - 94
2113LYSLYSPROPROOO22 - 1124 - 94
1114LYSLYSPROPROLL22 - 1124 - 94
2114LYSLYSPROPROPP22 - 1124 - 94
1115LYSLYSVALVALMM22 - 1114 - 93
2115LYSLYSVALVALNN22 - 1114 - 93
1116LYSLYSVALVALMM22 - 1114 - 93
2116LYSLYSVALVALOO22 - 1114 - 93
1117LYSLYSVALVALMM22 - 1114 - 93
2117LYSLYSVALVALPP22 - 1114 - 93
1118LYSLYSPROPRONN22 - 1124 - 94
2118LYSLYSPROPROOO22 - 1124 - 94
1119LYSLYSPROPRONN22 - 1124 - 94
2119LYSLYSPROPROPP22 - 1124 - 94
1120LYSLYSPROPROOO22 - 1124 - 94
2120LYSLYSPROPROPP22 - 1124 - 94

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
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Components

#1: Protein
Potassium channel protein,Cyclic nucleotide-gated olfactory channel,Potassium channel protein / Cyclic nucleotide-gated cation channel 2 / Cyclic nucleotide-gated channel alpha-2 / CNG2


Mass: 10294.113 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711) (bacteria), (gene. exp.) Homo sapiens (human)
Strain: ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711
Gene: BC_0669, CNGA2, CNCA, CNCA1, CNCG2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q81HW2, UniProt: Q16280
#2: Chemical...
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 40-44% MPD 100 mM MES pH 6.5 25mM Glycine

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.95389 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95389 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.914
11h,-k,-l20.086
ReflectionResolution: 2.63→67.62 Å / Num. obs: 44752 / % possible obs: 92.8 % / Redundancy: 3.6 % / CC1/2: 0.987 / Rmerge(I) obs: 0.19 / Net I/σ(I): 4.3
Reflection shellResolution: 2.63→2.68 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.97 / Num. unique obs: 2175 / CC1/2: 0.54 / % possible all: 91

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K0D
Resolution: 2.63→67.62 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.91 / SU B: 8.502 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R Free: 0.083 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26934 2291 5.1 %RANDOM
Rwork0.23534 ---
obs0.23708 42458 84.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.784 Å2
Baniso -1Baniso -2Baniso -3
1-20.56 Å20 Å26 Å2
2---18.53 Å20 Å2
3----2.02 Å2
Refinement stepCycle: 1 / Resolution: 2.63→67.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11672 0 68 95 11835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01311959
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711984
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.64916286
X-RAY DIFFRACTIONr_angle_other_deg1.2711.57327609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.96351448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.67923.234402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.617151854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg35.4781516
X-RAY DIFFRACTIONr_chiral_restr0.0610.21678
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212944
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022376
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_it4.5294.7226017
X-RAY DIFFRACTIONr_mcbond_other4.5284.7216015
X-RAY DIFFRACTIONr_mcangle_it6.6997.0477390
X-RAY DIFFRACTIONr_mcangle_other6.6987.0477390
X-RAY DIFFRACTIONr_scbond_it4.3165.0115942
X-RAY DIFFRACTIONr_scbond_other4.3155.0115943
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4717.3968897
X-RAY DIFFRACTIONr_long_range_B_refined10.99488.54148867
X-RAY DIFFRACTIONr_long_range_B_other10.9988.54448854
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)
11A29950.04
12B29950.04
21A29940.04
22C29940.04
31A30080.03
32D30080.03
41A30050.04
42E30050.04
51A29950.03
52F29950.03
61A30060.02
62G30060.02
71A30080.02
72H30080.02
81A29650.04
82I29650.04
91A29870.04
92J29870.04
101A29970.03
102K29970.03
111A29910.04
112L29910.04
121A29590.04
122M29590.04
131A29880.04
132N29880.04
141A29960.04
142O29960.04
151A29920.04
152P29920.04
161B29830.05
162C29830.05
171B29940.04
172D29940.04
181B29920.05
182E29920.05
191B29910.04
192F29910.04
201B29900.03
202G29900.03
211B30190.03
212H30190.03
221B29490.06
222I29490.06
231B29720.05
232J29720.05
241B29810.05
242K29810.05
251B29750.05
252L29750.05
261B29420.05
262M29420.05
271B29730.05
272N29730.05
281B29820.04
282O29820.04
291B29760.05
292P29760.05
301C30080.03
302D30080.03
311C29950.05
312E29950.05
321C29820.04
322F29820.04
331C30030.04
332G30030.04
341C29910.05
342H29910.05
351C29770.03
352I29770.03
361C30020.03
362J30020.03
371C30090.03
372K30090.03
381C30060.03
382L30060.03
391C29710.03
392M29710.03
401C30030.03
402N30030.03
411C29980.03
412O29980.03
421C30040.03
422P30040.03
431D30030.05
432E30030.05
441D29920.04
442F29920.04
451D30040.03
452G30040.03
461D30050.04
462H30050.04
471D29730.04
472I29730.04
481D29970.04
482J29970.04
491D30070.02
492K30070.02
501D30000.03
502L30000.03
511D29660.03
512M29660.03
521D29980.04
522N29980.04
531D30070.02
532O30070.02
541D30000.03
542P30000.03
551E29890.04
552F29890.04
561E29990.04
562G29990.04
571E30020.04
572H30020.04
581E29570.06
582I29570.06
591E29840.05
592J29840.05
601E29910.05
602K29910.05
611E29870.05
612L29870.05
621E29490.05
622M29490.05
631E29840.05
632N29840.05
641E29900.05
642O29900.05
651E29850.05
652P29850.05
661F29890.03
662G29890.03
671F29910.03
672H29910.03
681F29540.04
682I29540.04
691F29810.03
692J29810.03
701F29820.04
702K29820.04
711F29840.03
712L29840.03
721F29490.05
722M29490.05
731F29820.03
732N29820.03
741F29800.04
742O29800.04
751F29860.03
752P29860.03
761G30030.03
762H30030.03
771G29700.05
772I29700.05
781G29920.04
782J29920.04
791G30030.03
792K30030.03
801G29950.04
802L29950.04
811G29630.04
812M29630.04
821G29930.04
822N29930.04
831G29920.03
832O29920.03
841G29960.04
842P29960.04
851H29610.05
852I29610.05
861H29810.04
862J29810.04
871H29920.03
872K29920.03
881H29870.04
882L29870.04
891H29550.05
892M29550.05
901H29840.04
902N29840.04
911H29930.04
912O29930.04
921H29890.04
922P29890.04
931I29740.03
932J29740.03
941I29780.03
942K29780.03
951I29790.03
952L29790.03
961I30950.03
962M30950.03
971I29750.03
972N29750.03
981I29660.04
982O29660.04
991I29790.03
992P29790.03
1001J30500.04
1002K30500.04
1011J30530.03
1012L30530.03
1021J30160.04
1022M30160.04
1031J30640.02
1032N30640.02
1041J30470.04
1042O30470.04
1051J30500.03
1052P30500.03
1061K30060.02
1062L30060.02
1071K29720.03
1072M29720.03
1081K30010.03
1082N30010.03
1091K30050.03
1092O30050.03
1101K30060.02
1102P30060.02
1111L29730.03
1112M29730.03
1121L30090.02
1122N30090.02
1131L29960.04
1132O29960.04
1141L30070.01
1142P30070.01
1151M29690.04
1152N29690.04
1161M29630.03
1162O29630.03
1171M29720.03
1172P29720.03
1181N30030.03
1182O30030.03
1191N30050.02
1192P30050.02
1201O29930.04
1202P29930.04
LS refinement shellResolution: 2.549→2.615 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0 0 -
obs--0 %

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