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- PDB-9mr9: Crystal structure of AU-15330 in complex with the bromodomain of ... -

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Basic information

Entry
Database: PDB / ID: 9mr9
TitleCrystal structure of AU-15330 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB
Components
  • Elongin-B
  • Elongin-C
  • Isoform Short of Probable global transcription activator SNF2L2
  • von Hippel-Lindau disease tumor suppressor
KeywordsTRANSCRIPTION / SMARCA2 / VHL / PROTAC / ternary complex
Function / homology
Function and homology information


regulation of cellular response to hypoxia / bBAF complex / npBAF complex / nBAF complex / brahma complex / nucleosome array spacer activity / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / GBAF complex / regulation of G0 to G1 transition ...regulation of cellular response to hypoxia / bBAF complex / npBAF complex / nBAF complex / brahma complex / nucleosome array spacer activity / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / GBAF complex / regulation of G0 to G1 transition / transcription elongation factor activity / intermediate filament cytoskeleton / target-directed miRNA degradation / elongin complex / regulation of nucleotide-excision repair / Replication of the SARS-CoV-1 genome / VCB complex / Cul5-RING ubiquitin ligase complex / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / Cul2-RING ubiquitin ligase complex / positive regulation of T cell differentiation / intracellular membraneless organelle / positive regulation of double-strand break repair / SUMOylation of ubiquitinylation proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of stem cell population maintenance / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / negative regulation of transcription elongation by RNA polymerase II / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / negative regulation of cell differentiation / spermatid development / ATP-dependent activity, acting on DNA / positive regulation of myoblast differentiation / Tat-mediated elongation of the HIV-1 transcript / negative regulation of signal transduction / Formation of HIV-1 elongation complex containing HIV-1 Tat / ubiquitin-like ligase-substrate adaptor activity / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / negative regulation of TORC1 signaling / RNA Polymerase II Pre-transcription Events / negative regulation of autophagy / protein serine/threonine kinase binding / transcription corepressor binding / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / positive regulation of cell differentiation / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / helicase activity / negative regulation of cell growth / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Evasion by RSV of host interferon responses / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Regulation of expression of SLITs and ROBOs / RMTs methylate histone arginines / cell morphogenesis / ubiquitin-protein transferase activity / transcription corepressor activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / nervous system development / Neddylation / microtubule cytoskeleton / regulation of gene expression / protein-containing complex assembly / Replication of the SARS-CoV-2 genome / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / histone binding / molecular adaptor activity / cellular response to hypoxia / DNA-binding transcription factor binding / amyloid fibril formation / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / hydrolase activity / transcription cis-regulatory region binding / protein stabilization / protein ubiquitination / cilium / chromatin remodeling / negative regulation of cell population proliferation / negative regulation of gene expression / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / ubiquitin protein ligase binding / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process
Similarity search - Function
BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain ...BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / domain in helicases and associated with SANT domains / von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain / VHL box domain / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / Elongin-C / Elongin B / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / SKP1/BTB/POZ domain superfamily / Helicase conserved C-terminal domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / von Hippel-Lindau disease tumor suppressor / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsWang, M. / Xu, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cancer Res. / Year: 2025
Title: PRT3789 is a First-in-Human SMARCA2-Selective Degrader that Induces Synthetic Lethality in SMARCA4-Mutated Cancers.
Authors: Hulse, M. / Wang, M. / Xu, C. / Carter, J. / Agarwal, A. / Lu, L. / Pitis, P. / Bhagwat, N. / Rager, J. / Kurian, J. / Basch, C. / Sivakumar, M. / Burtell, J. / Mondal, A. / Grego, A. / ...Authors: Hulse, M. / Wang, M. / Xu, C. / Carter, J. / Agarwal, A. / Lu, L. / Pitis, P. / Bhagwat, N. / Rager, J. / Kurian, J. / Basch, C. / Sivakumar, M. / Burtell, J. / Mondal, A. / Grego, A. / Moore, A. / Bachner, C. / Vykuntam, K. / Reichelderfer, A. / Park, J. / Cote, J. / Cowart, M. / Osinubi, O.P. / Bigot, L. / Da Silva, A. / Nobre, C. / Meteau, M. / Soares, M. / Tang, H.Y. / Bersch, K. / Dai, C. / Cao, G. / Shen, B. / Emm, T. / Ruepp, S. / Xavier, J. / Tankersley, C. / Heiser, D. / Lee, S.H. / Geeganage, S. / Ruggeri, B. / Lin, H. / Novotny, W. / Huang, J. / Vaddi, K. / Combs, A. / Scherle, P. / Ito, K.
History
DepositionJan 7, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform Short of Probable global transcription activator SNF2L2
B: von Hippel-Lindau disease tumor suppressor
C: Elongin-C
D: Elongin-B
E: Isoform Short of Probable global transcription activator SNF2L2
F: von Hippel-Lindau disease tumor suppressor
G: Elongin-C
H: Elongin-B
I: Isoform Short of Probable global transcription activator SNF2L2
J: von Hippel-Lindau disease tumor suppressor
K: Elongin-C
L: Elongin-B
M: Isoform Short of Probable global transcription activator SNF2L2
N: von Hippel-Lindau disease tumor suppressor
O: Elongin-C
P: Elongin-B
Q: Isoform Short of Probable global transcription activator SNF2L2
R: von Hippel-Lindau disease tumor suppressor
S: Elongin-C
T: Elongin-B
U: Isoform Short of Probable global transcription activator SNF2L2
V: von Hippel-Lindau disease tumor suppressor
W: Elongin-C
X: Elongin-B
Y: Isoform Short of Probable global transcription activator SNF2L2
Z: von Hippel-Lindau disease tumor suppressor
a: Elongin-C
b: Elongin-B
c: Isoform Short of Probable global transcription activator SNF2L2
d: von Hippel-Lindau disease tumor suppressor
e: Elongin-C
f: Elongin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)450,16347
Polymers443,65132
Non-polymers6,51215
Water1,928107
1
A: Isoform Short of Probable global transcription activator SNF2L2
B: von Hippel-Lindau disease tumor suppressor
C: Elongin-C
D: Elongin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2746
Polymers55,4564
Non-polymers8182
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Isoform Short of Probable global transcription activator SNF2L2
F: von Hippel-Lindau disease tumor suppressor
G: Elongin-C
H: Elongin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3367
Polymers55,4564
Non-polymers8803
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Isoform Short of Probable global transcription activator SNF2L2
J: von Hippel-Lindau disease tumor suppressor
K: Elongin-C
L: Elongin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3667
Polymers55,4564
Non-polymers9103
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: Isoform Short of Probable global transcription activator SNF2L2
N: von Hippel-Lindau disease tumor suppressor
O: Elongin-C
P: Elongin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2125
Polymers55,4564
Non-polymers7561
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
Q: Isoform Short of Probable global transcription activator SNF2L2
R: von Hippel-Lindau disease tumor suppressor
S: Elongin-C
T: Elongin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2746
Polymers55,4564
Non-polymers8182
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
U: Isoform Short of Probable global transcription activator SNF2L2
V: von Hippel-Lindau disease tumor suppressor
W: Elongin-C
X: Elongin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2125
Polymers55,4564
Non-polymers7561
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
Y: Isoform Short of Probable global transcription activator SNF2L2
Z: von Hippel-Lindau disease tumor suppressor
a: Elongin-C
b: Elongin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2125
Polymers55,4564
Non-polymers7561
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
c: Isoform Short of Probable global transcription activator SNF2L2
d: von Hippel-Lindau disease tumor suppressor
e: Elongin-C
f: Elongin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2746
Polymers55,4564
Non-polymers8182
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.950, 298.503, 142.988
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
12A
22I
13A
23M
14A
24Q
15A
25U
16A
26Y
17A
27c
18B
28F
19B
29J
110B
210N
111B
211R
112B
212V
113B
213Z
114B
214d
115C
215G
116C
216K
117C
217O
118C
218S
119C
219W
120C
220a
121C
221e
122D
222H
123D
223L
124D
224P
125D
225T
126D
226X
127D
227b
128D
228f
129E
229I
130E
230M
131E
231Q
132E
232U
133E
233Y
134E
234c
135F
235J
136F
236N
137F
237R
138F
238V
139F
239Z
140F
240d
141G
241K
142G
242O
143G
243S
144G
244W
145G
245a
146G
246e
147H
247L
148H
248P
149H
249T
150H
250X
151H
251b
152H
252f
153I
253M
154I
254Q
155I
255U
156I
256Y
157I
257c
158J
258N
159J
259R
160J
260V
161J
261Z
162J
262d
163K
263O
164K
264S
165K
265W
166K
266a
167K
267e
168L
268P
169L
269T
170L
270X
171L
271b
172L
272f
173M
273Q
174M
274U
175M
275Y
176M
276c
177N
277R
178N
278V
179N
279Z
180N
280d
181O
281S
182O
282W
183O
283a
184O
284e
185P
285T
186P
286X
187P
287b
188P
288f
189Q
289U
190Q
290Y
191Q
291c
192R
292V
193R
293Z
194R
294d
195S
295W
196S
296a
197S
297e
198T
298X
199T
299b
1100T
2100f
1101U
2101Y
1102U
2102c
1103V
2103Z
1104V
2104d
1105W
2105a
1106W
2106e
1107X
2107b
1108X
2108f
1109Y
2109c
1110Z
2110d
1111a
2111e
1112b
2112f

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
11LEULEULYSLYSAA1376 - 14905 - 119
21LEULEULYSLYSEE1376 - 14905 - 119
12LEULEULYSLYSAA1376 - 14905 - 119
22LEULEULYSLYSII1376 - 14905 - 119
13LEULEULYSLYSAA1376 - 14905 - 119
23LEULEULYSLYSMM1376 - 14905 - 119
14LEULEULYSLYSAA1376 - 14905 - 119
24LEULEULYSLYSQQ1376 - 14905 - 119
15LEULEULYSLYSAA1376 - 14905 - 119
25LEULEULYSLYSUU1376 - 14905 - 119
16LEULEULYSLYSAA1376 - 14905 - 119
26LEULEULYSLYSYY1376 - 14905 - 119
17LEULEULYSLYSAA1376 - 14905 - 119
27LEULEULYSLYScCA1376 - 14905 - 119
18ARGARGGLNGLNBB60 - 2098 - 157
28ARGARGGLNGLNFF60 - 2098 - 157
19ARGARGGLNGLNBB60 - 2098 - 157
29ARGARGGLNGLNJJ60 - 2098 - 157
110ARGARGGLNGLNBB60 - 2098 - 157
210ARGARGGLNGLNNN60 - 2098 - 157
111ARGARGGLNGLNBB60 - 2098 - 157
211ARGARGGLNGLNRR60 - 2098 - 157
112ARGARGGLNGLNBB60 - 2098 - 157
212ARGARGGLNGLNVV60 - 2098 - 157
113ARGARGGLNGLNBB60 - 2098 - 157
213ARGARGGLNGLNZZ60 - 2098 - 157
114ARGARGGLNGLNBB60 - 2098 - 157
214ARGARGGLNGLNdDA60 - 2098 - 157
115METMETCYSCYSCC17 - 1121 - 96
215METMETCYSCYSGG17 - 1121 - 96
116METMETCYSCYSCC17 - 1121 - 96
216METMETCYSCYSKK17 - 1121 - 96
117METMETCYSCYSCC17 - 1121 - 96
217METMETCYSCYSOO17 - 1121 - 96
118METMETCYSCYSCC17 - 1121 - 96
218METMETCYSCYSSS17 - 1121 - 96
119METMETCYSCYSCC17 - 1121 - 96
219METMETCYSCYSWW17 - 1121 - 96
120METMETCYSCYSCC17 - 1121 - 96
220METMETCYSCYSaAA17 - 1121 - 96
121METMETCYSCYSCC17 - 1121 - 96
221METMETCYSCYSeEA17 - 1121 - 96
122METMETLYSLYSDD1 - 1041 - 104
222METMETLYSLYSHH1 - 1041 - 104
123METMETLYSLYSDD1 - 1041 - 104
223METMETLYSLYSLL1 - 1041 - 104
124METMETLYSLYSDD1 - 1041 - 104
224METMETLYSLYSPP1 - 1041 - 104
125METMETLYSLYSDD1 - 1041 - 104
225METMETLYSLYSTT1 - 1041 - 104
126METMETLYSLYSDD1 - 1041 - 104
226METMETLYSLYSXX1 - 1041 - 104
127METMETLYSLYSDD1 - 1041 - 104
227METMETLYSLYSbBA1 - 1041 - 104
128METMETLYSLYSDD1 - 1041 - 104
228METMETLYSLYSfFA1 - 1041 - 104
129LEULEUGLUGLUEE1376 - 14915 - 120
229LEULEUGLUGLUII1376 - 14915 - 120
130LEULEUGLUGLUEE1376 - 14915 - 120
230LEULEUGLUGLUMM1376 - 14915 - 120
131LEULEULYSLYSEE1376 - 14905 - 119
231LEULEULYSLYSQQ1376 - 14905 - 119
132LEULEULYSLYSEE1376 - 14905 - 119
232LEULEULYSLYSUU1376 - 14905 - 119
133LEULEULYSLYSEE1376 - 14905 - 119
233LEULEULYSLYSYY1376 - 14905 - 119
134LEULEULYSLYSEE1376 - 14905 - 119
234LEULEULYSLYScCA1376 - 14905 - 119
135PROPROGLNGLNFF59 - 2097 - 157
235PROPROGLNGLNJJ59 - 2097 - 157
136PROPROGLNGLNFF59 - 2097 - 157
236PROPROGLNGLNNN59 - 2097 - 157
137PROPROARGARGFF59 - 2107 - 158
237PROPROARGARGRR59 - 2107 - 158
138PROPROARGARGFF59 - 2107 - 158
238PROPROARGARGVV59 - 2107 - 158
139PROPROARGARGFF59 - 2107 - 158
239PROPROARGARGZZ59 - 2107 - 158
140PROPROARGARGFF59 - 2107 - 158
240PROPROARGARGdDA59 - 2107 - 158
141METMETCYSCYSGG17 - 1121 - 96
241METMETCYSCYSKK17 - 1121 - 96
142METMETCYSCYSGG17 - 1121 - 96
242METMETCYSCYSOO17 - 1121 - 96
143METMETCYSCYSGG17 - 1121 - 96
243METMETCYSCYSSS17 - 1121 - 96
144METMETCYSCYSGG17 - 1121 - 96
244METMETCYSCYSWW17 - 1121 - 96
145METMETCYSCYSGG17 - 1121 - 96
245METMETCYSCYSaAA17 - 1121 - 96
146METMETCYSCYSGG17 - 1121 - 96
246METMETCYSCYSeEA17 - 1121 - 96
147METMETLYSLYSHH1 - 1041 - 104
247METMETLYSLYSLL1 - 1041 - 104
148METMETLYSLYSHH1 - 1041 - 104
248METMETLYSLYSPP1 - 1041 - 104
149METMETLYSLYSHH1 - 1041 - 104
249METMETLYSLYSTT1 - 1041 - 104
150METMETLYSLYSHH1 - 1041 - 104
250METMETLYSLYSXX1 - 1041 - 104
151METMETLYSLYSHH1 - 1041 - 104
251METMETLYSLYSbBA1 - 1041 - 104
152METMETLYSLYSHH1 - 1041 - 104
252METMETLYSLYSfFA1 - 1041 - 104
153LEULEUGLUGLUII1376 - 14915 - 120
253LEULEUGLUGLUMM1376 - 14915 - 120
154LEULEULYSLYSII1376 - 14905 - 119
254LEULEULYSLYSQQ1376 - 14905 - 119
155LEULEULYSLYSII1376 - 14905 - 119
255LEULEULYSLYSUU1376 - 14905 - 119
156LEULEULYSLYSII1376 - 14905 - 119
256LEULEULYSLYSYY1376 - 14905 - 119
157LEULEULYSLYSII1376 - 14905 - 119
257LEULEULYSLYScCA1376 - 14905 - 119
158GLUGLUARGARGJJ55 - 2103 - 158
258GLUGLUARGARGNN55 - 2103 - 158
159PROPROGLNGLNJJ59 - 2097 - 157
259PROPROGLNGLNRR59 - 2097 - 157
160PROPROGLNGLNJJ59 - 2097 - 157
260PROPROGLNGLNVV59 - 2097 - 157
161PROPROGLNGLNJJ59 - 2097 - 157
261PROPROGLNGLNZZ59 - 2097 - 157
162PROPROGLNGLNJJ59 - 2097 - 157
262PROPROGLNGLNdDA59 - 2097 - 157
163METMETCYSCYSKK17 - 1121 - 96
263METMETCYSCYSOO17 - 1121 - 96
164METMETCYSCYSKK17 - 1121 - 96
264METMETCYSCYSSS17 - 1121 - 96
165METMETCYSCYSKK17 - 1121 - 96
265METMETCYSCYSWW17 - 1121 - 96
166METMETCYSCYSKK17 - 1121 - 96
266METMETCYSCYSaAA17 - 1121 - 96
167METMETCYSCYSKK17 - 1121 - 96
267METMETCYSCYSeEA17 - 1121 - 96
168METMETLYSLYSLL1 - 1041 - 104
268METMETLYSLYSPP1 - 1041 - 104
169METMETLYSLYSLL1 - 1041 - 104
269METMETLYSLYSTT1 - 1041 - 104
170METMETLYSLYSLL1 - 1041 - 104
270METMETLYSLYSXX1 - 1041 - 104
171METMETLYSLYSLL1 - 1041 - 104
271METMETLYSLYSbBA1 - 1041 - 104
172METMETLYSLYSLL1 - 1041 - 104
272METMETLYSLYSfFA1 - 1041 - 104
173LEULEULYSLYSMM1376 - 14905 - 119
273LEULEULYSLYSQQ1376 - 14905 - 119
174LEULEULYSLYSMM1376 - 14905 - 119
274LEULEULYSLYSUU1376 - 14905 - 119
175LEULEULYSLYSMM1376 - 14905 - 119
275LEULEULYSLYSYY1376 - 14905 - 119
176LEULEULYSLYSMM1376 - 14905 - 119
276LEULEULYSLYScCA1376 - 14905 - 119
177PROPROGLNGLNNN59 - 2097 - 157
277PROPROGLNGLNRR59 - 2097 - 157
178PROPROGLNGLNNN59 - 2097 - 157
278PROPROGLNGLNVV59 - 2097 - 157
179PROPROGLNGLNNN59 - 2097 - 157
279PROPROGLNGLNZZ59 - 2097 - 157
180PROPROGLNGLNNN59 - 2097 - 157
280PROPROGLNGLNdDA59 - 2097 - 157
181METMETCYSCYSOO17 - 1121 - 96
281METMETCYSCYSSS17 - 1121 - 96
182METMETCYSCYSOO17 - 1121 - 96
282METMETCYSCYSWW17 - 1121 - 96
183METMETCYSCYSOO17 - 1121 - 96
283METMETCYSCYSaAA17 - 1121 - 96
184METMETCYSCYSOO17 - 1121 - 96
284METMETCYSCYSeEA17 - 1121 - 96
185METMETLYSLYSPP1 - 1041 - 104
285METMETLYSLYSTT1 - 1041 - 104
186METMETLYSLYSPP1 - 1041 - 104
286METMETLYSLYSXX1 - 1041 - 104
187METMETLYSLYSPP1 - 1041 - 104
287METMETLYSLYSbBA1 - 1041 - 104
188METMETLYSLYSPP1 - 1041 - 104
288METMETLYSLYSfFA1 - 1041 - 104
189LEULEUGLUGLUQQ1376 - 14915 - 120
289LEULEUGLUGLUUU1376 - 14915 - 120
190LEULEUGLUGLUQQ1376 - 14935 - 122
290LEULEUGLUGLUYY1376 - 14935 - 122
191LEULEUGLUGLUQQ1376 - 14935 - 122
291LEULEUGLUGLUcCA1376 - 14935 - 122
192PROPROARGARGRR59 - 2107 - 158
292PROPROARGARGVV59 - 2107 - 158
193PROPROARGARGRR59 - 2107 - 158
293PROPROARGARGZZ59 - 2107 - 158
194PROPROARGARGRR59 - 2107 - 158
294PROPROARGARGdDA59 - 2107 - 158
195METMETCYSCYSSS17 - 1121 - 96
295METMETCYSCYSWW17 - 1121 - 96
196METMETCYSCYSSS17 - 1121 - 96
296METMETCYSCYSaAA17 - 1121 - 96
197METMETCYSCYSSS17 - 1121 - 96
297METMETCYSCYSeEA17 - 1121 - 96
198METMETLYSLYSTT1 - 1041 - 104
298METMETLYSLYSXX1 - 1041 - 104
199METMETLYSLYSTT1 - 1041 - 104
299METMETLYSLYSbBA1 - 1041 - 104
1100METMETLYSLYSTT1 - 1041 - 104
2100METMETLYSLYSfFA1 - 1041 - 104
1101LEULEUGLUGLUUU1376 - 14915 - 120
2101LEULEUGLUGLUYY1376 - 14915 - 120
1102LEULEUGLUGLUUU1376 - 14915 - 120
2102LEULEUGLUGLUcCA1376 - 14915 - 120
1103PROPROARGARGVV59 - 2107 - 158
2103PROPROARGARGZZ59 - 2107 - 158
1104PROPROARGARGVV59 - 2107 - 158
2104PROPROARGARGdDA59 - 2107 - 158
1105METMETCYSCYSWW17 - 1121 - 96
2105METMETCYSCYSaAA17 - 1121 - 96
1106METMETCYSCYSWW17 - 1121 - 96
2106METMETCYSCYSeEA17 - 1121 - 96
1107METMETLYSLYSXX1 - 1041 - 104
2107METMETLYSLYSbBA1 - 1041 - 104
1108METMETLYSLYSXX1 - 1041 - 104
2108METMETLYSLYSfFA1 - 1041 - 104
1109LEULEUGLUGLUYY1376 - 14935 - 122
2109LEULEUGLUGLUcCA1376 - 14935 - 122
1110PROPROARGARGZZ59 - 2107 - 158
2110PROPROARGARGdDA59 - 2107 - 158
1111METMETCYSCYSaAA17 - 1121 - 96
2111METMETCYSCYSeEA17 - 1121 - 96
1112METMETLYSLYSbBA1 - 1041 - 104
2112METMETLYSLYSfFA1 - 1041 - 104

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

-
Components

-
Protein , 4 types, 32 molecules AEIMQUYcBFJNRVZdCGKOSWaeDHLPTXbf

#1: Protein
Isoform Short of Probable global transcription activator SNF2L2 / ATP-dependent helicase SMARCA2 / BRG1-associated factor 190B / BAF190B / Protein brahma homolog / ...ATP-dependent helicase SMARCA2 / BRG1-associated factor 190B / BAF190B / Protein brahma homolog / hBRM / SNF2-alpha / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2


Mass: 14249.347 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA2, BAF190B, BRM, SNF2A, SNF2L2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P51531, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein
von Hippel-Lindau disease tumor suppressor / Protein G7 / pVHL


Mass: 18615.215 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VHL / Production host: Escherichia coli (E. coli) / References: UniProt: P40337
#3: Protein
Elongin-C / EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / ...EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Transcription elongation factor B polypeptide 1


Mass: 10843.420 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15369
#4: Protein
Elongin-B / EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / ...EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Transcription elongation factor B polypeptide 2


Mass: 11748.406 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15370

-
Non-polymers , 4 types, 122 molecules

#5: Chemical
ChemComp-A1BNT / N-({4-[(6M)-3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl}acetyl)-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide


Mass: 755.929 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C39H49N9O5S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.05~0.2 M sodium formate, 0.1 M HEPES, pH 7.5~8.5, 10%~24% w/v PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12713 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 3.3→29.87 Å / Num. obs: 70695 / % possible obs: 99 % / Redundancy: 4.1 % / CC1/2: 0.981 / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.171 / Rrim(I) all: 0.267 / Net I/σ(I): 5.4
Reflection shellResolution: 3.3→3.37 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.19 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4624 / CC1/2: 0.503 / Rpim(I) all: 0.989 / Rrim(I) all: 1.554 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.28data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→29.87 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.872 / SU B: 41.535 / SU ML: 0.63 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.63 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2752 3501 5 %RANDOM
Rwork0.2188 ---
obs0.2216 67156 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 295.59 Å2 / Biso mean: 90.333 Å2 / Biso min: 12.23 Å2
Baniso -1Baniso -2Baniso -3
1--3.39 Å20 Å2-0.91 Å2
2--1.98 Å2-0 Å2
3---1.41 Å2
Refinement stepCycle: final / Resolution: 3.3→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30397 0 462 107 30966
Biso mean--59.6 42.3 -
Num. residues----3759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01331592
X-RAY DIFFRACTIONr_bond_other_d0.0010.01530349
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.67942807
X-RAY DIFFRACTIONr_angle_other_deg1.1781.59770030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.10853735
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.65121.5211768
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.411155599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.73515274
X-RAY DIFFRACTIONr_chiral_restr0.0890.24065
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0235092
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027212
X-RAY DIFFRACTIONr_mcbond_it5.0829.62915021
X-RAY DIFFRACTIONr_mcbond_other5.0819.62815020
X-RAY DIFFRACTIONr_mcangle_it8.53114.42318726
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A36700.14
12E36700.14
21A36150.15
22I36150.15
31A35340.16
32M35340.16
41A35610.16
42Q35610.16
51A32290.24
52U32290.24
61A36300.14
62Y36300.14
71A34910.15
72c34910.15
81B47320.1
82F47320.1
91B46930.11
92J46930.11
101B46990.11
102N46990.11
111B46930.11
112R46930.11
121B46140.13
122V46140.13
131B46480.12
132Z46480.12
141B45980.12
142d45980.12
151C27370.12
152G27370.12
161C27780.12
162K27780.12
171C27520.12
172O27520.12
181C27410.14
182S27410.14
191C27170.13
192W27170.13
201C27510.13
202a27510.13
211C27370.12
212e27370.12
221D28170.15
222H28170.15
231D29230.12
232L29230.12
241D29220.12
242P29220.12
251D28390.14
252T28390.14
261D28840.13
262X28840.13
271D29510.09
272b29510.09
281D29460.09
282f29460.09
291E35810.17
292I35810.17
301E35190.16
302M35190.16
311E35260.17
312Q35260.17
321E32060.24
322U32060.24
331E36070.15
332Y36070.15
341E34740.16
342c34740.16
351F47200.11
352J47200.11
361F47290.11
362N47290.11
371F47570.11
372R47570.11
381F46810.13
382V46810.13
391F47190.11
392Z47190.11
401F46670.11
402d46670.11
411G27650.11
412K27650.11
421G27710.11
422O27710.11
431G27340.13
432S27340.13
441G27500.12
442W27500.12
451G27350.13
452a27350.13
461G27540.1
462e27540.1
471H27860.15
472L27860.15
481H27920.15
482P27920.15
491H27680.15
492T27680.15
501H27490.16
502X27490.16
511H28150.13
512b28150.13
521H28110.13
522f28110.13
531I35620.16
532M35620.16
541I35140.17
542Q35140.17
551I32240.23
552U32240.23
561I35550.16
562Y35550.16
571I34540.16
572c34540.16
581J48690.1
582N48690.1
591J47170.11
592R47170.11
601J46410.13
602V46410.13
611J46750.11
612Z46750.11
621J46520.11
622d46520.11
631K28100.09
632O28100.09
641K27980.12
642S27980.12
651K27600.12
652W27600.12
661K27840.12
662a27840.12
671K27730.1
672e27730.1
681L29130.11
682P29130.11
691L28190.13
692T28190.13
701L28680.13
702X28680.13
711L29120.1
712b29120.1
721L29060.1
722f29060.1
731M34720.18
732Q34720.18
741M32080.23
742U32080.23
751M34850.17
752Y34850.17
761M34180.17
762c34180.17
771N47420.12
772R47420.12
781N46430.14
782V46430.14
791N47020.12
792Z47020.12
801N46640.11
802d46640.11
811O27560.12
812S27560.12
821O27670.1
822W27670.1
831O27630.12
832a27630.12
841O27910.1
842e27910.1
851P28220.13
852T28220.13
861P28890.12
862X28890.12
871P29150.1
872b29150.1
881P29080.09
882f29080.09
891Q32670.24
892U32670.24
901Q36110.17
902Y36110.17
911Q34900.18
912c34900.18
921R46740.12
922V46740.12
931R46960.12
932Z46960.12
941R46530.12
942d46530.12
951S27260.13
952W27260.13
961S27500.12
962a27500.12
971S27290.12
972e27290.12
981T27950.14
982X27950.14
991T28660.11
992b28660.11
1001T28510.11
1002f28510.11
1011U32460.23
1012Y32460.23
1021U32100.22
1022c32100.22
1031V46070.14
1032Z46070.14
1041V45720.14
1042d45720.14
1051W27280.13
1052a27280.13
1061W27370.12
1062e27370.12
1071X29000.1
1072b29000.1
1081X28880.1
1082f28880.1
1091Y36290.15
1092c36290.15
1101Z46340.12
1102d46340.12
1111a27630.1
1112e27630.1
1121b29790.05
1122f29790.05
LS refinement shellResolution: 3.3→3.386 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 251 -
Rwork0.335 5043 -
all-5294 -
obs--99.74 %

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