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- PDB-4c3e: HRSV M2-1 mutant S58D S61D, P21 crystal -

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Basic information

Entry
Database: PDB / ID: 4c3e
TitleHRSV M2-1 mutant S58D S61D, P21 crystal
ComponentsMATRIX M2-1
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


regulation of viral transcription / Respiratory syncytial virus genome transcription / Translation of respiratory syncytial virus mRNAs / Respiratory syncytial virus genome replication / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / viral transcription / Respiratory syncytial virus (RSV) attachment and entry / virion component ...regulation of viral transcription / Respiratory syncytial virus genome transcription / Translation of respiratory syncytial virus mRNAs / Respiratory syncytial virus genome replication / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / viral transcription / Respiratory syncytial virus (RSV) attachment and entry / virion component / transcription antitermination / host cell cytoplasm / host cell nucleus / structural molecule activity / RNA binding / metal ion binding
Similarity search - Function
Pneumovirus matrix protein 2 (M2), zinc-binding domain / Pneumovirus matrix 2-1 / Pneumovirus matrix protein 2 (M2) / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHUMAN RESPIRATORY SYNCYTIAL VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTanner, S.J. / Ariza, A. / Richard, C.A. / Wu, W. / Trincao, J. / Hiscox, J.A. / Carroll, M.W. / Silman, N.J. / Eleouet, J.F. / Edwards, T.A. / Barr, J.N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Crystal Structure of the Essential Transcription Antiterminator M2-1 Protein of Human Respiratory Syncytial Virus and Implications of its Phosphorylation.
Authors: Tanner, S.J. / Ariza, A. / Richard, C. / Kyle, H.F. / Dods, R.L. / Blondot, M. / Wu, W. / Trincao, J. / Trinh, C.H. / Hiscox, J.A. / Carroll, M.W. / Silman, N.J. / Eleouet, J. / Edwards, T.A. / Barr, J.N.
History
DepositionAug 22, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MATRIX M2-1
B: MATRIX M2-1
C: MATRIX M2-1
D: MATRIX M2-1
E: MATRIX M2-1
F: MATRIX M2-1
G: MATRIX M2-1
H: MATRIX M2-1
I: MATRIX M2-1
J: MATRIX M2-1
K: MATRIX M2-1
L: MATRIX M2-1
M: MATRIX M2-1
N: MATRIX M2-1
O: MATRIX M2-1
P: MATRIX M2-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)363,57132
Polymers362,52516
Non-polymers1,04716
Water7,116395
1
B: MATRIX M2-1
H: MATRIX M2-1
I: MATRIX M2-1
L: MATRIX M2-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8938
Polymers90,6314
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13660 Å2
ΔGint-43.3 kcal/mol
Surface area32740 Å2
MethodPISA
2
D: MATRIX M2-1
J: MATRIX M2-1
K: MATRIX M2-1
M: MATRIX M2-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8938
Polymers90,6314
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13680 Å2
ΔGint-43.3 kcal/mol
Surface area32560 Å2
MethodPISA
3
A: MATRIX M2-1
C: MATRIX M2-1
E: MATRIX M2-1
F: MATRIX M2-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8938
Polymers90,6314
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13530 Å2
ΔGint-43.5 kcal/mol
Surface area34790 Å2
MethodPISA
4
G: MATRIX M2-1
N: MATRIX M2-1
O: MATRIX M2-1
P: MATRIX M2-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8938
Polymers90,6314
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13380 Å2
ΔGint-43.2 kcal/mol
Surface area34990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.680, 141.600, 142.160
Angle α, β, γ (deg.)90.00, 93.92, 90.00
Int Tables number4
Space group name H-MP1211
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
11SERSERILEILEAA2 - 1737 - 178
21SERSERILEILEBB2 - 1737 - 178
12GLYGLYILEILEAA-1 - 1734 - 178
22GLYGLYILEILECC-1 - 1734 - 178
13ARGARGILEILEAA3 - 1738 - 178
23ARGARGILEILEDD3 - 1738 - 178
14GLYGLYASNASNAA-1 - 1744 - 179
24GLYGLYASNASNEE-1 - 1744 - 179
15GLYGLYASNASNAA-1 - 1744 - 179
25GLYGLYASNASNFF-1 - 1744 - 179
16GLYGLYASNASNAA-1 - 1744 - 179
26GLYGLYASNASNGG-1 - 1744 - 179
17ARGARGILEILEAA4 - 1739 - 178
27ARGARGILEILEHH4 - 1739 - 178
18ARGARGILEILEAA4 - 1739 - 178
28ARGARGILEILEII4 - 1739 - 178
19ARGARGILEILEAA4 - 1739 - 178
29ARGARGILEILEJJ4 - 1739 - 178
110ARGARGILEILEAA3 - 1738 - 178
210ARGARGILEILEKK3 - 1738 - 178
111ARGARGILEILEAA4 - 1739 - 178
211ARGARGILEILELL4 - 1739 - 178
112ARGARGASNASNAA4 - 1749 - 179
212ARGARGASNASNMM4 - 1749 - 179
113LEULEUASNASNAA-2 - 1743 - 179
213LEULEUASNASNNN-2 - 1743 - 179
114GLYGLYASNASNAA-1 - 1744 - 179
214GLYGLYASNASNOO-1 - 1744 - 179
115GLYGLYASNASNAA-1 - 1744 - 179
215GLYGLYASNASNPP-1 - 1744 - 179
116SERSERILEILEBB2 - 1737 - 178
216SERSERILEILECC2 - 1737 - 178
117ARGARGILEILEBB3 - 1738 - 178
217ARGARGILEILEDD3 - 1738 - 178
118SERSERASNASNBB2 - 1747 - 179
218SERSERASNASNEE2 - 1747 - 179
119SERSERASNASNBB2 - 1747 - 179
219SERSERASNASNFF2 - 1747 - 179
120SERSERASNASNBB2 - 1747 - 179
220SERSERASNASNGG2 - 1747 - 179
121ARGARGASNASNBB4 - 1749 - 179
221ARGARGASNASNHH4 - 1749 - 179
122ARGARGASNASNBB4 - 1749 - 179
222ARGARGASNASNII4 - 1749 - 179
123ARGARGILEILEBB4 - 1739 - 178
223ARGARGILEILEJJ4 - 1739 - 178
124ARGARGASNASNBB3 - 1748 - 179
224ARGARGASNASNKK3 - 1748 - 179
125ARGARGASNASNBB4 - 1749 - 179
225ARGARGASNASNLL4 - 1749 - 179
126ARGARGASNASNBB4 - 1749 - 179
226ARGARGASNASNMM4 - 1749 - 179
127SERSERILEILEBB2 - 1737 - 178
227SERSERILEILENN2 - 1737 - 178
128SERSERASNASNBB2 - 1747 - 179
228SERSERASNASNOO2 - 1747 - 179
129SERSERASNASNBB2 - 1747 - 179
229SERSERASNASNPP2 - 1747 - 179
130ARGARGILEILECC3 - 1738 - 178
230ARGARGILEILEDD3 - 1738 - 178
131GLYGLYASNASNCC-1 - 1744 - 179
231GLYGLYASNASNEE-1 - 1744 - 179
132GLYGLYASNASNCC-1 - 1744 - 179
232GLYGLYASNASNFF-1 - 1744 - 179
133GLYGLYASNASNCC-1 - 1744 - 179
233GLYGLYASNASNGG-1 - 1744 - 179
134ARGARGILEILECC4 - 1739 - 178
234ARGARGILEILEHH4 - 1739 - 178
135ARGARGILEILECC4 - 1739 - 178
235ARGARGILEILEII4 - 1739 - 178
136ARGARGILEILECC4 - 1739 - 178
236ARGARGILEILEJJ4 - 1739 - 178
137ARGARGILEILECC3 - 1738 - 178
237ARGARGILEILEKK3 - 1738 - 178
138ARGARGILEILECC4 - 1739 - 178
238ARGARGILEILELL4 - 1739 - 178
139ARGARGASNASNCC4 - 1749 - 179
239ARGARGASNASNMM4 - 1749 - 179
140GLYGLYASNASNCC-1 - 1744 - 179
240GLYGLYASNASNNN-1 - 1744 - 179
141GLYGLYASNASNCC-1 - 1744 - 179
241GLYGLYASNASNOO-1 - 1744 - 179
142GLYGLYASNASNCC-1 - 1744 - 179
242GLYGLYASNASNPP-1 - 1744 - 179
143ARGARGASNASNDD3 - 1748 - 179
243ARGARGASNASNEE3 - 1748 - 179
144ARGARGASNASNDD3 - 1748 - 179
244ARGARGASNASNFF3 - 1748 - 179
145ARGARGASNASNDD3 - 1748 - 179
245ARGARGASNASNGG3 - 1748 - 179
146ARGARGASNASNDD4 - 1749 - 179
246ARGARGASNASNHH4 - 1749 - 179
147ARGARGASNASNDD4 - 1749 - 179
247ARGARGASNASNII4 - 1749 - 179
148ARGARGILEILEDD4 - 1739 - 178
248ARGARGILEILEJJ4 - 1739 - 178
149ARGARGASNASNDD3 - 1748 - 179
249ARGARGASNASNKK3 - 1748 - 179
150ARGARGASNASNDD4 - 1749 - 179
250ARGARGASNASNLL4 - 1749 - 179
151ARGARGASNASNDD4 - 1749 - 179
251ARGARGASNASNMM4 - 1749 - 179
152ARGARGILEILEDD3 - 1738 - 178
252ARGARGILEILENN3 - 1738 - 178
153ARGARGILEILEDD3 - 1738 - 178
253ARGARGILEILEOO3 - 1738 - 178
154ARGARGASNASNDD3 - 1748 - 179
254ARGARGASNASNPP3 - 1748 - 179
155GLYGLYASNASNEE-1 - 1744 - 179
255GLYGLYASNASNFF-1 - 1744 - 179
156GLYGLYASNASNEE-1 - 1744 - 179
256GLYGLYASNASNGG-1 - 1744 - 179
157ARGARGASNASNEE4 - 1749 - 179
257ARGARGASNASNHH4 - 1749 - 179
158ARGARGASNASNEE4 - 1749 - 179
258ARGARGASNASNII4 - 1749 - 179
159ARGARGASNASNEE4 - 1749 - 179
259ARGARGASNASNJJ4 - 1749 - 179
160ARGARGASNASNEE3 - 1748 - 179
260ARGARGASNASNKK3 - 1748 - 179
161ARGARGASNASNEE4 - 1749 - 179
261ARGARGASNASNLL4 - 1749 - 179
162ARGARGILEILEEE4 - 1739 - 178
262ARGARGILEILEMM4 - 1739 - 178
163GLYGLYASNASNEE-1 - 1744 - 179
263GLYGLYASNASNNN-1 - 1744 - 179
164GLYGLYASNASNEE-1 - 1744 - 179
264GLYGLYASNASNOO-1 - 1744 - 179
165GLYGLYASNASNEE-1 - 1744 - 179
265GLYGLYASNASNPP-1 - 1744 - 179
166GLYGLYASNASNFF-1 - 1744 - 179
266GLYGLYASNASNGG-1 - 1744 - 179
167ARGARGASNASNFF4 - 1749 - 179
267ARGARGASNASNHH4 - 1749 - 179
168ARGARGASNASNFF4 - 1749 - 179
268ARGARGASNASNII4 - 1749 - 179
169ARGARGASNASNFF4 - 1749 - 179
269ARGARGASNASNJJ4 - 1749 - 179
170ARGARGASNASNFF3 - 1748 - 179
270ARGARGASNASNKK3 - 1748 - 179
171ARGARGASNASNFF4 - 1749 - 179
271ARGARGASNASNLL4 - 1749 - 179
172ARGARGILEILEFF4 - 1739 - 178
272ARGARGILEILEMM4 - 1739 - 178
173GLYGLYASNASNFF-1 - 1744 - 179
273GLYGLYASNASNNN-1 - 1744 - 179
174GLYGLYASNASNFF-1 - 1744 - 179
274GLYGLYASNASNOO-1 - 1744 - 179
175GLYGLYASNASNFF-1 - 1744 - 179
275GLYGLYASNASNPP-1 - 1744 - 179
176ARGARGILEILEGG4 - 1739 - 178
276ARGARGILEILEHH4 - 1739 - 178
177ARGARGILEILEGG4 - 1739 - 178
277ARGARGILEILEII4 - 1739 - 178
178ARGARGILEILEGG4 - 1739 - 178
278ARGARGILEILEJJ4 - 1739 - 178
179ARGARGILEILEGG3 - 1738 - 178
279ARGARGILEILEKK3 - 1738 - 178
180ARGARGILEILEGG4 - 1739 - 178
280ARGARGILEILELL4 - 1739 - 178
181ARGARGASNASNGG4 - 1749 - 179
281ARGARGASNASNMM4 - 1749 - 179
182GLYGLYASNASNGG-1 - 1744 - 179
282GLYGLYASNASNNN-1 - 1744 - 179
183GLYGLYASNASNGG-1 - 1744 - 179
283GLYGLYASNASNOO-1 - 1744 - 179
184GLYGLYASNASNGG-1 - 1744 - 179
284GLYGLYASNASNPP-1 - 1744 - 179
185ARGARGASNASNHH4 - 1749 - 179
285ARGARGASNASNII4 - 1749 - 179
186ARGARGASNASNHH4 - 1749 - 179
286ARGARGASNASNJJ4 - 1749 - 179
187ARGARGASNASNHH4 - 1749 - 179
287ARGARGASNASNKK4 - 1749 - 179
188ARGARGASNASNHH4 - 1749 - 179
288ARGARGASNASNLL4 - 1749 - 179
189ARGARGASNASNHH4 - 1749 - 179
289ARGARGASNASNMM4 - 1749 - 179
190ARGARGILEILEHH4 - 1739 - 178
290ARGARGILEILENN4 - 1739 - 178
191ARGARGILEILEHH4 - 1739 - 178
291ARGARGILEILEOO4 - 1739 - 178
192ARGARGASNASNHH4 - 1749 - 179
292ARGARGASNASNPP4 - 1749 - 179
193ARGARGASNASNII4 - 1749 - 179
293ARGARGASNASNJJ4 - 1749 - 179
194ARGARGILEILEII4 - 1739 - 178
294ARGARGILEILEKK4 - 1739 - 178
195ARGARGASNASNII4 - 1749 - 179
295ARGARGASNASNLL4 - 1749 - 179
196ARGARGASNASNII4 - 1749 - 179
296ARGARGASNASNMM4 - 1749 - 179
197ARGARGILEILEII4 - 1739 - 178
297ARGARGILEILENN4 - 1739 - 178
198ARGARGILEILEII4 - 1739 - 178
298ARGARGILEILEOO4 - 1739 - 178
199ARGARGASNASNII4 - 1749 - 179
299ARGARGASNASNPP4 - 1749 - 179
1100ARGARGASNASNJJ4 - 1749 - 179
2100ARGARGASNASNKK4 - 1749 - 179
1101ARGARGASNASNJJ4 - 1749 - 179
2101ARGARGASNASNLL4 - 1749 - 179
1102ARGARGASNASNJJ4 - 1749 - 179
2102ARGARGASNASNMM4 - 1749 - 179
1103ARGARGILEILEJJ4 - 1739 - 178
2103ARGARGILEILENN4 - 1739 - 178
1104ARGARGILEILEJJ4 - 1739 - 178
2104ARGARGILEILEOO4 - 1739 - 178
1105ARGARGASNASNJJ4 - 1749 - 179
2105ARGARGASNASNPP4 - 1749 - 179
1106ARGARGASNASNKK4 - 1749 - 179
2106ARGARGASNASNLL4 - 1749 - 179
1107ARGARGASNASNKK4 - 1749 - 179
2107ARGARGASNASNMM4 - 1749 - 179
1108ARGARGILEILEKK3 - 1738 - 178
2108ARGARGILEILENN3 - 1738 - 178
1109ARGARGILEILEKK3 - 1738 - 178
2109ARGARGILEILEOO3 - 1738 - 178
1110ARGARGASNASNKK3 - 1748 - 179
2110ARGARGASNASNPP3 - 1748 - 179
1111ARGARGASNASNLL4 - 1749 - 179
2111ARGARGASNASNMM4 - 1749 - 179
1112ARGARGILEILELL4 - 1739 - 178
2112ARGARGILEILENN4 - 1739 - 178
1113ARGARGILEILELL4 - 1739 - 178
2113ARGARGILEILEOO4 - 1739 - 178
1114ARGARGASNASNLL4 - 1749 - 179
2114ARGARGASNASNPP4 - 1749 - 179
1115ARGARGASNASNMM4 - 1749 - 179
2115ARGARGASNASNNN4 - 1749 - 179
1116ARGARGASNASNMM4 - 1749 - 179
2116ARGARGASNASNOO4 - 1749 - 179
1117ARGARGILEILEMM4 - 1739 - 178
2117ARGARGILEILEPP4 - 1739 - 178
1118GLYGLYASNASNNN-1 - 1744 - 179
2118GLYGLYASNASNOO-1 - 1744 - 179
1119GLYGLYASNASNNN-1 - 1744 - 179
2119GLYGLYASNASNPP-1 - 1744 - 179
1120GLYGLYASNASNOO-1 - 1744 - 179
2120GLYGLYASNASNPP-1 - 1744 - 179

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
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120

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Components

#1: Protein
MATRIX M2-1 / ENVELOPE-ASSOCIATED 22 KDA PROTEIN / HRSV M2-1


Mass: 22657.799 Da / Num. of mol.: 16 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN RESPIRATORY SYNCYTIAL VIRUS / Strain: A2 / Plasmid: PGEX-6P / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: P04545
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.38 % / Description: NONE
Crystal growpH: 8.5
Details: 20 % (V/V) PEG MME 2000, 0.2 M TRIMETHYLAMINE N-OXIDE, 0.1 M TRIS PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9889
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2013 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9889 Å / Relative weight: 1
ReflectionResolution: 2.4→78.12 Å / Num. obs: 138151 / % possible obs: 100 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.1
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.4 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→78.24 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.35 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.354 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23769 6851 5 %RANDOM
Rwork0.20347 ---
obs0.20515 131263 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.588 Å2
Baniso -1Baniso -2Baniso -3
1-2.32 Å20 Å20.08 Å2
2---0.97 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 2.4→78.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21315 0 16 395 21726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01921963
X-RAY DIFFRACTIONr_bond_other_d0.0090.0221870
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.95929596
X-RAY DIFFRACTIONr_angle_other_deg1.505350281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.48652685
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93723.9321058
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.091154335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.70815184
X-RAY DIFFRACTIONr_chiral_restr0.0960.23360
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0224476
X-RAY DIFFRACTIONr_gen_planes_other0.0080.025116
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_it4.6124.53410602
X-RAY DIFFRACTIONr_mcbond_other4.6114.53410601
X-RAY DIFFRACTIONr_mcangle_it6.9116.76913216
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.7555.3511361
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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)
11A103510.04
12B103510.04
21A104600.04
22C104600.04
31A103720.03
32D103720.03
41A97360.04
42E97360.04
51A97450.04
52F97450.04
61A101690.04
62G101690.04
71A100880.04
72H100880.04
81A100770.04
82I100770.04
91A102950.02
92J102950.02
101A101950.04
102K101950.04
111A100690.04
112L100690.04
121A95690.03
122M95690.03
131A103540.05
132N103540.05
141A102910.03
142O102910.03
151A97640.03
152P97640.03
161B104500.04
162C104500.04
171B104340.04
172D104340.04
181B96490.05
182E96490.05
191B96560.05
192F96560.05
201B101540.04
202G101540.04
211B102090.04
212H102090.04
221B101700.05
222I101700.05
231B103510.04
232J103510.04
241B103110.04
242K103110.04
251B101720.05
252L101720.05
261B95870.05
262M95870.05
271B102000.05
272N102000.05
281B102480.04
282O102480.04
291B97200.04
292P97200.04
301C104120.03
302D104120.03
311C97720.04
312E97720.04
321C97780.04
322F97780.04
331C102430.04
332G102430.04
341C101500.04
342H101500.04
351C101180.04
352I101180.04
361C103600.03
362J103600.03
371C102520.04
372K102520.04
381C101430.04
382L101430.04
391C95890.04
392M95890.04
401C103120.04
402N103120.04
411C103780.03
412O103780.03
421C98460.03
422P98460.03
431D96550.04
432E96550.04
441D96640.04
442F96640.04
451D101330.04
452G101330.04
461D102310.03
462H102310.03
471D101800.04
472I101800.04
481D103860.03
482J103860.03
491D103550.03
492K103550.03
501D101790.04
502L101790.04
511D95950.04
512M95950.04
521D101990.04
522N101990.04
531D102310.03
532O102310.03
541D97290.03
542P97290.03
551E98180.04
552F98180.04
561E97820.04
562G97820.04
571E95770.04
572H95770.04
581E95640.04
582I95640.04
591E95640.04
592J95640.04
601E96400.04
602K96400.04
611E95620.05
612L95620.05
621E96080.03
622M96080.03
631E97170.04
632N97170.04
641E97910.03
642O97910.03
651E98090.03
652P98090.03
661F98110.05
662G98110.05
671F96110.05
672H96110.05
681F95800.04
682I95800.04
691F95810.04
692J95810.04
701F96710.04
702K96710.04
711F95820.05
712L95820.05
721F96280.03
722M96280.03
731F97500.05
732N97500.05
741F98130.04
742O98130.04
751F98330.03
752P98330.03
761G100170.03
762H100170.03
771G99370.05
772I99370.05
781G99710.04
782J99710.04
791G100660.04
792K100660.04
801G99780.05
802L99780.05
811G95380.05
812M95380.05
821G101400.05
822N101400.05
831G102460.03
832O102460.03
841G98130.04
842P98130.04
851H101720.04
852I101720.04
861H101810.04
862J101810.04
871H102150.03
872K102150.03
881H101960.04
882L101960.04
891H96060.04
892M96060.04
901H101230.04
902N101230.04
911H101570.03
912O101570.03
921H96440.03
922P96440.03
931I101410.04
932J101410.04
941I101360.04
942K101360.04
951I101230.05
952L101230.05
961I95750.04
962M95750.04
971I101840.01
972N101840.01
981I100820.03
982O100820.03
991I95840.04
992P95840.04
1001J102000.04
1002K102000.04
1011J101770.04
1012L101770.04
1021J95890.04
1022M95890.04
1031J100780.05
1032N100780.05
1041J101220.03
1042O101220.03
1051J96230.03
1052P96230.03
1061K101910.04
1062L101910.04
1071K95860.04
1072M95860.04
1081K102100.04
1082N102100.04
1091K102370.03
1092O102370.03
1101K97260.03
1102P97260.03
1111L96000.05
1112M96000.05
1121L100700.05
1122N100700.05
1131L101500.04
1132O101500.04
1141L96280.04
1142P96280.04
1151M95440.04
1152N95440.04
1161M95740.04
1162O95740.04
1171M95530.03
1172P95530.03
1181N103030.04
1182O103030.04
1191N97690.04
1192P97690.04
1201O98480.02
1202P98480.02
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 507 -
Rwork0.284 9648 -
obs--99.63 %

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