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8GXS: PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state

PDB ID:

8GXS Download

MMDB ID:

222621

PDB Deposition Date:

2022/9/21

Updated in MMDB:

2022/11

Experimental Method:

electron microscopy

Resolution:

4.16 Å

Source Organism:

synthetic construct▼

Taxonomy	Molecule
synthetic construct	X, Y, NX, NY
Sus scrofa	PA, PB, PC, PE, PF, PH, PI, PJ, PK, PL, PD, PG
Homo sapiens	BA, DA, EA, FA, HA, DB, EB, FB, HB, HC, DO, DP, DQ, HD, HG, HE, HF, HH, DD, DE, DF, DG, DH, DI, DL, Dc, Dd, De, Df, Di, Dj, Dk, Dl, Dm, HI, HJ, g, j, n, s, u, a, d, f, i, m, q, z, b, c, e, l, o, h , k, r, t, v, p, w, x, y, DJ, NC , NG
Xenopus laevis	NA, NB, ND, NE, NF, NH

Similar Structures:

Biological Unit for 8GXS: 87-meric; determined by author

Molecular Components in 8GXS
Label	Count	Molecule
Proteins (83 molecules)
BA	1	Transcription Initiation Factor IIB
DA	1	Transcription Initiation Factor Tfiid Subunit 1
EA	1	General Transcription Factor IIE Subunit 1
FA	1	General Transcription Factor IIF Subunit 1
HA	1	General Transcription and DNA Repair Factor IIH Helicase Subunit XPD
NA NE	2	Histone H3
PA	1	DNA-directed RNA Polymerase Subunit
DB	1	Transcription Initiation Factor Tfiid Subunit 2
EB	1	Transcription Initiation Factor IIE Subunit Beta
FB	1	General Transcription Factor IIF Subunit 2
HB	1	General Transcription Factor IIH Subunit 1
NB NF	2	Histone H4
PB	1	DNA-directed RNA Polymerase Subunit Beta
HC	1	General Transcription Factor IIH Subunit 4
DO	1	Transcription Initiation Factor IIA Subunit 2
DP	1	Tata-box-binding Protein
DQ	1	Transcription Initiation Factor IIA Subunit 1
PC	1	DNA-directed RNA Polymerase II Subunit Rpb3
PE	1	DNA-directed RNA Polymerase II Subunit E
PF	1	DNA-directed RNA Polymerase II Subunit F
PH	1	DNA-directed RNA Polymerases I, II, and III Subunit Rpabc3
PI	1	DNA-directed RNA Polymerase II Subunit Rpb9
PJ	1	DNA-directed RNA Polymerases I, II, and III Subunit Rpabc5
PK	1	RNA_pol_l_2 Domain-containing Protein
PL	1	Rpb12
HD	1	Cdk-activating Kinase Assembly Factor Mat1
HG	1	General Transcription Factor IIH Subunit 2
HE	1	General Transcription Factor IIH Subunit 3
HF	1	General Transcription Factor IIH Subunit 5
HH	1	General Transcription and DNA Repair Factor IIH Helicase Subunit XPB
DD Dd	2	Transcription Initiation Factor Tfiid Subunit 4
DE De	2	Transcription Initiation Factor Tfiid Subunit 5
DF Df	2	Transcription Initiation Factor Tfiid Subunit 6
DG	1	Transcription Initiation Factor Tfiid Subunit 7
DH	1	Transcription Initiation Factor Tfiid Subunit 8
DI Di	2	Transcription Initiation Factor Tfiid Subunit 9
DL Dl	2	Transcription Initiation Factor Tfiid Subunit 12
Dc	1	Transcription Initiation Factor Tfiid Subunit 3
Dj DJ	2	Transcription Initiation Factor Tfiid Subunit 10
Dk	1	Transcription Initiation Factor Tfiid Subunit 11
Dm	1	Transcription Initiation Factor Tfiid Subunit 13
HI	1	Cyclin-dependent Kinase 7
HJ	1	Cyclin-h
PD	1	DNA-directed RNA Polymerase II Subunit Rpb4
PG	1	DNA-directed RNA Polymerase II Subunit Rpb7
g	1	Mediator of RNA Polymerase II Transcription Subunit 7
j	1	Mediator of RNA Polymerase II Transcription Subunit 10
n	1	Mediator of RNA Polymerase II Transcription Subunit 14
s	1	Mediator of RNA Polymerase II Transcription Subunit 19
u	1	Mediator of RNA Polymerase II Transcription Subunit 21
a	1	Mediator of RNA Polymerase II Transcription Subunit 1
d	1	Mediator of RNA Polymerase II Transcription Subunit 4
f	1	Mediator of RNA Polymerase II Transcription Subunit 6
i	1	Mediator of RNA Polymerase II Transcription Subunit 9
m	1	Mediator of RNA Polymerase II Transcription Subunit 31
q	1	Mediator of RNA Polymerase II Transcription Subunit 17
z	1	Mediator of RNA Polymerase II Transcription Subunit 26
b	1	Mediator of RNA Polymerase II Transcription Subunit 29
c	1	Mediator of RNA Polymerase II Transcription Subunit 27
e	1	Mediator of RNA Polymerase II Transcription Subunit 28
l	1	Mediator of RNA Polymerase II Transcription Subunit 30
o	1	Mediator of RNA Polymerase II Transcription Subunit 15
h	1	Isoform 2 of Mediator of RNA Polymerase II Transcription Subunit 8
k	1	Mediator of RNA Polymerase II Transcription Subunit 11
r	1	Mediator of RNA Polymerase II Transcription Subunit 18
t	1	Mediator of RNA Polymerase II Transcription Subunit 20
v	1	Mediator of RNA Polymerase II Transcription Subunit 22
p	1	Isoform 2 of Mediator of RNA Polymerase II Transcription Subunit 16
w	1	Mediator of RNA Polymerase II Transcription Subunit 23
x	1	Mediator of RNA Polymerase II Transcription Subunit 24
y	1	Mediator of RNA Polymerase II Transcription Subunit 25
NC NG	2	Histone H2a.z
ND NH	2	Histone H2B
Nucleotides(4 molecules)
X	1	DNA (228-mer)
Y	1	DNA (228-mer)
NX	1	DNA (162-mer)
NY	1	DNA (162-mer)
Chemicals and Non-standard biopolymers (21 molecules)
1	19	ZINC ION (Link to PubChem not yet available)
2	1	IRON/SULFUR CLUSTER (Link to PubChem not yet available)
3	1	MAGNESIUM ION (Link to PubChem not yet available)

* Click molecule labels to explore molecular sequence information.

Citing MMDB

Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303