8XJV | pdb_00008xjv

Structural basis for the linker histone H5-nucleosome binding and chromatin compaction


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ZC [auth An]SCOP2B SuperfamilyWinged helix DNA-binding domain 8002931 3000034 SCOP2B (2022-06-29)
YC [auth Am]SCOP2B SuperfamilyWinged helix DNA-binding domain 8002931 3000034 SCOP2B (2022-06-29)
XC [auth Al]SCOP2B SuperfamilyWinged helix DNA-binding domain 8002931 3000034 SCOP2B (2022-06-29)
WC [auth Ak]SCOP2B SuperfamilyWinged helix DNA-binding domain 8002931 3000034 SCOP2B (2022-06-29)
VC [auth Aj]SCOP2B SuperfamilyWinged helix DNA-binding domain 8002931 3000034 SCOP2B (2022-06-29)
UC [auth Ai]SCOP2B SuperfamilyWinged helix DNA-binding domain 8002931 3000034 SCOP2B (2022-06-29)
TC [auth Ah]SCOP2B SuperfamilyWinged helix DNA-binding domain 8002931 3000034 SCOP2B (2022-06-29)
ED [auth As]SCOP2B SuperfamilyWinged helix DNA-binding domain 8002931 3000034 SCOP2B (2022-06-29)
DD [auth Ar]SCOP2B SuperfamilyWinged helix DNA-binding domain 8002931 3000034 SCOP2B (2022-06-29)
CD [auth Aq]SCOP2B SuperfamilyWinged helix DNA-binding domain 8002931 3000034 SCOP2B (2022-06-29)
BD [auth Ap]SCOP2B SuperfamilyWinged helix DNA-binding domain 8002931 3000034 SCOP2B (2022-06-29)
AD [auth Ao]SCOP2B SuperfamilyWinged helix DNA-binding domain 8002931 3000034 SCOP2B (2022-06-29)
ZA [auth x]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
YA [auth w]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
XA [auth v]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
UB [auth a9]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
TB [auth a8]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
SB [auth a7]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
RB [auth a6]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
QB [auth a5]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
PB [auth a4]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
OB [auth a3]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
NB [auth a2]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
MB [auth CD]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
LB [auth 9]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
KB [auth 8]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
JB [auth 7]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
IB [auth 6]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
HB [auth 5]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
GB [auth 4]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
FB [auth 3]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
EB [auth 2]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
DB [auth 1]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
CB [auth 0]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
BB [auth z]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
AB [auth y]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
Z [auth X]SCOP2B SuperfamilyCore histone-like 8096712 3001387 SCOP2B (2022-06-29)
WA [auth u]SCOP2B SuperfamilyCore histone-like 8096712 3001387 SCOP2B (2022-06-29)
VA [auth t]SCOP2B SuperfamilyCore histone-like 8096712 3001387 SCOP2B (2022-06-29)
UA [auth s]SCOP2B SuperfamilyCore histone-like 8096712 3001387 SCOP2B (2022-06-29)
TA [auth r]SCOP2B SuperfamilyCore histone-like 8096712 3001387 SCOP2B (2022-06-29)
SA [auth q]SCOP2B SuperfamilyCore histone-like 8096712 3001387 SCOP2B (2022-06-29)
RA [auth p]SCOP2B SuperfamilyCore histone-like 8096712 3001387 SCOP2B (2022-06-29)
QA [auth o]SCOP2B SuperfamilyCore histone-like 8096712 3001387 SCOP2B (2022-06-29)
PA [auth n]SCOP2B SuperfamilyCore histone-like 8096712 3001387 SCOP2B (2022-06-29)
OA [auth m]SCOP2B SuperfamilyCore histone-like 8096712 3001387 SCOP2B (2022-06-29)
NA [auth l]SCOP2B SuperfamilyCore histone-like 8096712 3001387 SCOP2B (2022-06-29)
MA [auth k]SCOP2B SuperfamilyCore histone-like 8096712 3001387 SCOP2B (2022-06-29)
LA [auth j]SCOP2B SuperfamilyCore histone-like 8096712 3001387 SCOP2B (2022-06-29)
KA [auth i]SCOP2B SuperfamilyCore histone-like 8096712 3001387 SCOP2B (2022-06-29)
JA [auth h]SCOP2B SuperfamilyCore histone-like 8096712 3001387 SCOP2B (2022-06-29)
IA [auth g]SCOP2B SuperfamilyCore histone-like 8096712 3001387 SCOP2B (2022-06-29)
HA [auth f]SCOP2B SuperfamilyCore histone-like 8096712 3001387 SCOP2B (2022-06-29)
GA [auth e]SCOP2B SuperfamilyCore histone-like 8096712 3001387 SCOP2B (2022-06-29)
FA [auth d]SCOP2B SuperfamilyCore histone-like 8096712 3001387 SCOP2B (2022-06-29)
EA [auth c]SCOP2B SuperfamilyCore histone-like 8096712 3001387 SCOP2B (2022-06-29)
DA [auth b]SCOP2B SuperfamilyCore histone-like 8096712 3001387 SCOP2B (2022-06-29)
CA [auth a]SCOP2B SuperfamilyCore histone-like 8096712 3001387 SCOP2B (2022-06-29)
BA [auth Z]SCOP2B SuperfamilyCore histone-like 8096712 3001387 SCOP2B (2022-06-29)
AA [auth Y]SCOP2B SuperfamilyCore histone-like 8096712 3001387 SCOP2B (2022-06-29)
Y [auth W]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
X [auth V]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
W [auth U]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
V [auth T]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
U [auth S]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
T [auth R]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
SC [auth Ag]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
S [auth Q]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
RC [auth Af]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
R [auth P]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
Q [auth O]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
PC [auth Ad]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
P [auth N]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
OC [auth Ac]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
O [auth M]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
NC [auth Ab]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
MC [auth Aa]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
LC [auth az]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
L [auth J]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
KC [auth ay]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
JC [auth ax]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
IC [auth aw]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
HC [auth av]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
FD [auth At]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
ZB [auth an]SCOP2B SuperfamilyCore histone-like 8067126 3001387 SCOP2B (2022-06-29)
YB [auth am]SCOP2B SuperfamilyCore histone-like 8067126 3001387 SCOP2B (2022-06-29)
XB [auth al]SCOP2B SuperfamilyCore histone-like 8067126 3001387 SCOP2B (2022-06-29)
WB [auth ak]SCOP2B SuperfamilyCore histone-like 8067126 3001387 SCOP2B (2022-06-29)
VB [auth aj]SCOP2B SuperfamilyCore histone-like 8067126 3001387 SCOP2B (2022-06-29)
QC [auth Ae]SCOP2B SuperfamilyCore histone-like 8067126 3001387 SCOP2B (2022-06-29)
N [auth L]SCOP2B SuperfamilyCore histone-like 8067126 3001387 SCOP2B (2022-06-29)
M [auth K]SCOP2B SuperfamilyCore histone-like 8067126 3001387 SCOP2B (2022-06-29)
K [auth I]SCOP2B SuperfamilyCore histone-like 8067126 3001387 SCOP2B (2022-06-29)
J [auth H]SCOP2B SuperfamilyCore histone-like 8067126 3001387 SCOP2B (2022-06-29)
I [auth G]SCOP2B SuperfamilyCore histone-like 8067126 3001387 SCOP2B (2022-06-29)
H [auth F]SCOP2B SuperfamilyCore histone-like 8067126 3001387 SCOP2B (2022-06-29)
GC [auth au]SCOP2B SuperfamilyCore histone-like 8067126 3001387 SCOP2B (2022-06-29)
G [auth E]SCOP2B SuperfamilyCore histone-like 8067126 3001387 SCOP2B (2022-06-29)
FC [auth at]SCOP2B SuperfamilyCore histone-like 8067126 3001387 SCOP2B (2022-06-29)
F [auth D]SCOP2B SuperfamilyCore histone-like 8067126 3001387 SCOP2B (2022-06-29)
EC [auth as]SCOP2B SuperfamilyCore histone-like 8067126 3001387 SCOP2B (2022-06-29)
E [auth C]SCOP2B SuperfamilyCore histone-like 8067126 3001387 SCOP2B (2022-06-29)
DC [auth ar]SCOP2B SuperfamilyCore histone-like 8067126 3001387 SCOP2B (2022-06-29)
D [auth B]SCOP2B SuperfamilyCore histone-like 8067126 3001387 SCOP2B (2022-06-29)
CC [auth aq]SCOP2B SuperfamilyCore histone-like 8067126 3001387 SCOP2B (2022-06-29)
C [auth A]SCOP2B SuperfamilyCore histone-like 8067126 3001387 SCOP2B (2022-06-29)
BC [auth ap]SCOP2B SuperfamilyCore histone-like 8067126 3001387 SCOP2B (2022-06-29)
AC [auth ao]SCOP2B SuperfamilyCore histone-like 8067126 3001387 SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF15511Centromere kinetochore component CENP-T histone fold (CENP-T_C)Centromere kinetochore component CENP-T histone foldCENP-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 ...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 associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin [2-3].
Domain
PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain
PF16211C-terminus of histone H2A (Histone_H2A_C)C-terminus of histone H2A- Family
PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Histone H5
Histone H4
Histone H3 -
Histone H2B 1.1 -
Histone H2A
B [auth Av]DNA---
A [auth Au]DNA---

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
IPR005818Linker histone H1/H5, domain H15Domain
IPR005819Linker histone H1/H5Family
IPR009072Histone-foldHomologous Superfamily
IPR001951Histone H4Family
IPR035425CENP-T/Histone H4, histone foldDomain
IPR019809Histone H4, conserved siteConserved Site
IPR004823TATA box binding protein associated factor (TAF), histone-like fold domainDomain
IPR009072Histone-foldHomologous Superfamily
IPR000164Histone H3/CENP-AFamily
IPR007125Core Histone H2A/H2B/H3 domainDomain
IPR009072Histone-foldHomologous Superfamily
IPR055333Histone H2B, conserved siteConserved Site
IPR000558Histone H2BFamily
IPR007125Core Histone H2A/H2B/H3 domainDomain
IPR009072Histone-foldHomologous Superfamily
IPR002119Histone H2AFamily
IPR032454Histone H2A, C-terminal domainDomain
IPR032458Histone H2A conserved siteConserved Site
IPR007125Core Histone H2A/H2B/H3 domainDomain