8JHO
Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with di-nucleosome
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
Q [auth a] | SCOP2B Superfamily | Core histone-like | 8041272 | 3001387 | SCOP2B (2021-05-27) |
U [auth e] | SCOP2B Superfamily | Core histone-like | 8041272 | 3001387 | SCOP2B (2021-05-27) |
A | SCOP2B Superfamily | Core histone-like | 8041272 | 3001387 | SCOP2B (2021-05-27) |
E | SCOP2B Superfamily | Core histone-like | 8041272 | 3001387 | SCOP2B (2021-05-27) |
F | SCOP2B Superfamily | Core histone-like | 8042439 | 3001387 | SCOP2B (2021-05-27) |
B | SCOP2B Superfamily | Core histone-like | 8042439 | 3001387 | SCOP2B (2021-05-27) |
R [auth b] | SCOP2B Superfamily | Core histone-like | 8042439 | 3001387 | SCOP2B (2021-05-27) |
V [auth f] | SCOP2B Superfamily | Core histone-like | 8042439 | 3001387 | SCOP2B (2021-05-27) |
C | SCOP2B Superfamily | Core histone-like | 8041278 | 3001387 | SCOP2B (2021-05-27) |
G | SCOP2B Superfamily | Core histone-like | 8041278 | 3001387 | SCOP2B (2021-05-27) |
S [auth c] | SCOP2B Superfamily | Core histone-like | 8041278 | 3001387 | SCOP2B (2021-05-27) |
W [auth g] | SCOP2B Superfamily | Core histone-like | 8041278 | 3001387 | SCOP2B (2021-05-27) |
X [auth h] | SCOP2B Superfamily | Core histone-like | 8041279 | 3001387 | SCOP2B (2021-05-27) |
D | SCOP2B Superfamily | Core histone-like | 8041279 | 3001387 | SCOP2B (2021-05-27) |
H | SCOP2B Superfamily | Core histone-like | 8041279 | 3001387 | SCOP2B (2021-05-27) |
T [auth d] | SCOP2B Superfamily | Core histone-like | 8041279 | 3001387 | SCOP2B (2021-05-27) |
M | SCOP2B Superfamily | Chromo domain-like | 8089214 | 3000161 | SCOP2B (2021-05-27) |
O | SCOP2B Superfamily | Chromo domain-like | 8089214 | 3000161 | SCOP2B (2021-05-27) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
Q [auth a] | PF00125 | e8jhoa1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125 | ECOD (1.6) |
U [auth e] | PF00125 | e8jhoe1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125 | ECOD (1.6) |
A | PF00125 | e8jhoA1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125 | ECOD (1.6) |
E | PF00125 | e8jhoE1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125 | ECOD (1.6) |
F | PF15511 | e8jhoF1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF15511 | ECOD (1.6) |
B | PF15511 | e8jhoB1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF15511 | ECOD (1.6) |
R [auth b] | PF15511 | e8jhob1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF15511 | ECOD (1.6) |
V [auth f] | PF15511 | e8jhof1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF15511 | ECOD (1.6) |
C | PF00125,PF16211 | e8jhoC1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125,PF16211 | ECOD (1.6) |
G | PF00125,PF16211 | e8jhoG1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125,PF16211 | ECOD (1.6) |
S [auth c] | PF00125,PF16211 | e8jhoc1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125,PF16211 | ECOD (1.6) |
W [auth g] | PF00125,PF16211 | e8jhog1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125,PF16211 | ECOD (1.6) |
X [auth h] | PF00125 | e8jhoh1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125 | ECOD (1.6) |
D | PF00125 | e8jhoD1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125 | ECOD (1.6) |
H | PF00125 | e8jhoH1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125 | ECOD (1.6) |
T [auth d] | PF00125 | e8jhod1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: PF00125 | ECOD (1.6) |
L | PF00850 | e8jhoL1 | A: a/b three-layered sandwiches | X: HAD domain-like | H: HAD domain-related | T: Arginase/deacetylase | F: PF00850 | ECOD (1.6) |
M | PF22732 | e8jhoM2 | A: beta barrels | X: SH3 | H: Chromo domain-like (From Topology) | T: Chromo domain-like | F: PF22732 | ECOD (1.6) |
M | PF05712 | e8jhoM1 | A: alpha arrays | X: MRG domain (From Topology) | H: MRG domain (From Topology) | T: MRG domain | F: PF05712 | ECOD (1.6) |
O | PF22732 | e8jhoO2 | A: beta barrels | X: SH3 | H: Chromo domain-like (From Topology) | T: Chromo domain-like | F: PF22732 | ECOD (1.6) |
O | PF05712 | e8jhoO1 | A: alpha arrays | X: MRG domain (From Topology) | H: MRG domain (From Topology) | T: MRG domain | F: PF05712 | ECOD (1.6) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
A, E, Q [auth a], U [auth e] | PF00125 | Core histone H2A/H2B/H3/H4 (Histone) | Core histone H2A/H2B/H3/H4 | - | Domain |
B, F, R [auth b], V [auth f] | PF15511 | Centromere kinetochore component CENP-T histone fold (CENP-T_C) | Centromere kinetochore component CENP-T histone fold | CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly asso ... | Domain |
C, G, S [auth c], W [auth g] | PF16211 | C-terminus of histone H2A (Histone_H2A_C) | C-terminus of histone H2A | - | Family |
PF08295 | Sin3 family co-repressor (Sin3_corepress) | Sin3 family co-repressor | This domain is found on transcriptional regulators. It forms interactions with histone deacetylases [1]. | Domain | |
PF02671 | Paired amphipathic helix repeat (PAH) | Paired amphipathic helix repeat | - | Repeat | |
PF16879 | C-terminal domain of Sin3a protein (Sin3a_C) | C-terminal domain of Sin3a protein | - | Family | |
PF00850 | Histone deacetylase domain (Hist_deacetyl) | Histone deacetylase domain | Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins [1]. ... | Domain | |
PF11717 | RNA binding activity-knot of a chromodomain (Tudor-knot) | RNA binding activity-knot of a chromodomain | - | Family | |
PF22732 | MSL3 chromodomain-like (MSL3_chromo-like) | MSL3 chromodomain-like | This domain is found in Male-specific lethal-3 (MSL3) and other related proteins such as MRG15 transcription factor. MSL3 resides in the MSL (male-specific lethal) complex, which upregulates transcription by spreading the histone H4 Lys16 acetyl mark ... | Domain | |
PF00628 | PHD-finger (PHD) | PHD-finger | PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains [2]. Several PHD fingers have been identified as binding modules of methylated histone H3 [3]. | Domain |