8XGC

Structure of yeast replisome associated with FACT and histone hexamer, Composite map

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
T [auth L]SCOP2B SuperfamilyPH domain-like 8103650 3000134 SCOP2B (2022-06-29)
T [auth L]SCOP2B SuperfamilyPH domain-like 8103656 3000134 SCOP2B (2022-06-29)
U [auth M]SCOP2B SuperfamilyPH domain-like 8051654 3000134 SCOP2B (2022-06-29)
U [auth M]SCOP2B SuperfamilyPH domain-like 8103655 3000134 SCOP2B (2022-06-29)
U [auth M]SCOP2B SuperfamilyPH domain-like 8041841 3000134 SCOP2B (2022-06-29)
AA [auth S]SCOP2B SuperfamilyCore histone-like 8036586 3001387 SCOP2B (2022-06-29)
W [auth O]SCOP2B SuperfamilyCore histone-like 8036586 3001387 SCOP2B (2022-06-29)
X [auth P]SCOP2B SuperfamilyCore histone-like 8036588 3001387 SCOP2B (2022-06-29)
Y [auth Q]SCOP2B SuperfamilyCore histone-like 8036590 3001387 SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
K [auth C]PF05916GINS complex protein helical bundle domain (Sld5)GINS complex protein helical bundle domainThis entry represents the C-terminal alpha helical bundle domain. The eukaryotic GINS complex is essential for the initiation and elongation phases of DNA replication [1-3]. It consists of four paralogous protein subunits (Sld5, Psf1, Psf2 and Psf3) ...This entry represents the C-terminal alpha helical bundle domain. The eukaryotic GINS complex is essential for the initiation and elongation phases of DNA replication [1-3]. It consists of four paralogous protein subunits (Sld5, Psf1, Psf2 and Psf3), all of which are included in this family. The GINS complex is conserved from yeast to humans, and has been shown in human to bind directly to DNA primase [4].
Domain
K [auth C]PF22466GINS/PriA/YqbF domain (GINS_N)GINS/PriA/YqbF domainThis entry represents the GINS/PriA/YqbF domain, which is found in the N-terminal region of the GINS complex protein. The GINS complex is crucial for the establishment of DNA replication forks and replisome progression in eukaryotes. The crystal stru ...This entry represents the GINS/PriA/YqbF domain, which is found in the N-terminal region of the GINS complex protein. The GINS complex is crucial for the establishment of DNA replication forks and replisome progression in eukaryotes. The crystal structure of the human GINS complex reveals a heterotetrameric assembly with a pseudo symmetrical layered structure. The complex consists of two heterodimers that create four subunit-subunit interfaces. The subunit structures of the heterodimers consist of two alternating domains, an alpha-helix-rich (A) domain Pfam:PF05916 and a beta-strand-rich (B) domain (this entry).
Domain
L [auth D]PF05916GINS complex protein helical bundle domain (Sld5)GINS complex protein helical bundle domainThis entry represents the C-terminal alpha helical bundle domain. The eukaryotic GINS complex is essential for the initiation and elongation phases of DNA replication [1-3]. It consists of four paralogous protein subunits (Sld5, Psf1, Psf2 and Psf3) ...This entry represents the C-terminal alpha helical bundle domain. The eukaryotic GINS complex is essential for the initiation and elongation phases of DNA replication [1-3]. It consists of four paralogous protein subunits (Sld5, Psf1, Psf2 and Psf3), all of which are included in this family. The GINS complex is conserved from yeast to humans, and has been shown in human to bind directly to DNA primase [4].
Domain
L [auth D]PF16922DNA replication complex GINS protein SLD5 C-terminus (SLD5_C)DNA replication complex GINS protein SLD5 C-terminusThe C-terminal domain of DNA replication complex GINS protein SLD5 is important in the assembly of the GINS complex, a complex which is involved in initiation of DNA replication and progression of DNA replication forks [1].Domain
M [auth E]PF02724CDC45-like protein (CDC45)CDC45-like protein- Family
N [auth F],
O [auth G],
P [auth H]		PF12341Minichromosome loss protein, Mcl1, middle region (Mcl1_mid)Minichromosome loss protein, Mcl1, middle region- Repeat
N [auth F],
O [auth G],
P [auth H]		PF20946DNA polymerase alpha-binding protein Ctf4, C-terminal domain (Ctf4_C)DNA polymerase alpha-binding protein Ctf4, C-terminal domainThis domain is found at the C-terminal end of DNA polymerase alpha- binding protein Ctf4 from yeast, its human orthologue AND1, and similar proteins from eukaryotes. This accessory factor for DNA replication plays a role in accurately duplicating the ...This domain is found at the C-terminal end of DNA polymerase alpha- binding protein Ctf4 from yeast, its human orthologue AND1, and similar proteins from eukaryotes. This accessory factor for DNA replication plays a role in accurately duplicating the genome in vivo. This domain folds into a helical extension that is linked to the beta-propeller domain (Pfam:PF12341) and protrudes from one face of the disk-shaped trimer formed by the protein. It is essential for binding of dynamic partner proteins, such as Pol alpha-primase [1-4].
Domain
Q [auth I]PF04821Timeless protein (TIMELESS)Timeless protein- Family
R [auth J]PF07962Replication Fork Protection Component Swi3 (Swi3)Replication Fork Protection Component Swi3- Family
T [auth L]PF08644FACT complex subunit (SPT16/CDC68) (SPT16)FACT complex subunit (SPT16/CDC68)Proteins in this family are subunits the FACT complex. The FACT complex plays a role in transcription initiation and promotes binding of TATA-binding protein (TBP) to a TATA box in chromatin [2].Domain
T [auth L]PF08512Histone chaperone Rttp106-like, middle domain (Rttp106-like_middle)Histone chaperone Rttp106-like, middle domainThis Pleckstrin homology (PH) domain is found in the middle region of Rttp106, a histone chaperone involved in heterochromatin-mediated silencing [1]. It is also found in the final part of the middle domain of various FACT (facilitates chromatin tran ...This Pleckstrin homology (PH) domain is found in the middle region of Rttp106, a histone chaperone involved in heterochromatin-mediated silencing [1]. It is also found in the final part of the middle domain of various FACT (facilitates chromatin transactions) complex subunits, such as Spt16 and either Pob3 (yeast) or the related SSRP1 (higher eukaryotes). This domain plays a role in DNA binding [2-4].
Domain
T [auth L]PF21091FACT complex subunit SPT16, C-terminal domain (SPT16_C)FACT complex subunit SPT16, C-terminal domainFACT (facilitates chromatin transactions) is a general chromatin factor that acts to reorganise nucleosomes. SPT16 is a subunit of this complex that is conserved among eukaryotes, from yeast to humans. This entry represents the C-terminal domain of S ...FACT (facilitates chromatin transactions) is a general chromatin factor that acts to reorganise nucleosomes. SPT16 is a subunit of this complex that is conserved among eukaryotes, from yeast to humans. This entry represents the C-terminal domain of SPT16, which wraps around the DNA binding surface of H2A-H2B [1,2].
Domain
U [auth M]PF03531Structure-specific recognition protein (SSRP1) (SSrecog)Structure-specific recognition protein (SSRP1)SSRP1 has been implicated in transcriptional initiation and elongation and in DNA replication and repair [1]. This domain belongs to the Pleckstrin homology fold superfamily.Domain
U [auth M]PF08512Histone chaperone Rttp106-like, middle domain (Rttp106-like_middle)Histone chaperone Rttp106-like, middle domainThis Pleckstrin homology (PH) domain is found in the middle region of Rttp106, a histone chaperone involved in heterochromatin-mediated silencing [1]. It is also found in the final part of the middle domain of various FACT (facilitates chromatin tran ...This Pleckstrin homology (PH) domain is found in the middle region of Rttp106, a histone chaperone involved in heterochromatin-mediated silencing [1]. It is also found in the final part of the middle domain of various FACT (facilitates chromatin transactions) complex subunits, such as Spt16 and either Pob3 (yeast) or the related SSRP1 (higher eukaryotes). This domain plays a role in DNA binding [2-4].
Domain
U [auth M]PF17292POB3-like N-terminal PH domain (POB3_N)POB3-like N-terminal PH domainThis domain is found at the N-terminus of POB3 and related proteins.Domain
B [auth 3]PF00493MCM P-loop domain (MCM)MCM P-loop domain- Domain
B [auth 3]PF14551MCM N-terminal domain (MCM_N)MCM N-terminal domainThis family contains the N-terminal domain of MCM proteins.Domain
B [auth 3]PF17855MCM AAA-lid domain (MCM_lid)MCM AAA-lid domainThis entry represents the AAA-lid domain found in MCM proteins.Domain
B [auth 3]PF17207MCM OB domain (MCM_OB)MCM OB domainThis family contains an OB-fold found within MCM proteins. This domain contains an insertion at the zinc binding motif [2].Domain
X [auth P]PF16211C-terminus of histone H2A (Histone_H2A_C)C-terminus of histone H2A- Family
C [auth 4]PF00493MCM P-loop domain (MCM)MCM P-loop domain- Domain
C [auth 4]PF14551MCM N-terminal domain (MCM_N)MCM N-terminal domainThis family contains the N-terminal domain of MCM proteins.Domain
C [auth 4]PF17855MCM AAA-lid domain (MCM_lid)MCM AAA-lid domainThis entry represents the AAA-lid domain found in MCM proteins.Domain
C [auth 4]PF17207MCM OB domain (MCM_OB)MCM OB domainThis family contains an OB-fold found within MCM proteins. This domain contains an insertion at the zinc binding motif [2].Domain
C [auth 4]PF21128MCM4, winged helix domain (MCM4_WHD)MCM4, winged helix domainDNA replication licensing factor MCM4 is a component of the MCM2-MCM7 complex which consists of six sequence-related AAA+ type ATPases/helicases that form a heterohexameric ring essential for 'once per cell cycle' DNA replication initiation and elon ...DNA replication licensing factor MCM4 is a component of the MCM2-MCM7 complex which consists of six sequence-related AAA+ type ATPases/helicases that form a heterohexameric ring essential for 'once per cell cycle' DNA replication initiation and elongation in eukaryotic cells [1-3]. This is the winged helix domain (WHD) found at the C-terminal of MCM4 [1-3]. Upon ssDNA binding the MCM5-WHD moves out of the central channel and becomes disordered, the MCM6-WHD moves backward and away from the channel, and the MCM4-WHD now partially occludes the channel opening. These changes enable CMG (Cdc45, Mcm2-7, GINS, the eukaryotic replicative helicase) to encircle dsDNA, and is consistent with reports that showed the MCM2-7 matures into two fully assembled CMGs on dsDNA before origin DNA unwinding occurs [3].
Domain
D [auth 5]PF00493MCM P-loop domain (MCM)MCM P-loop domain- Domain
D [auth 5]PF14551MCM N-terminal domain (MCM_N)MCM N-terminal domainThis family contains the N-terminal domain of MCM proteins.Domain
D [auth 5]PF21933MCM5, C-terminal domain (MCM5_C)MCM5, C-terminal domainThis entry represents the C-terminal domain of MCM5 from humans and its homologues, which is a HTH domain [1]. MCM5 is part of the MCM2-7 complex.Domain
D [auth 5]PF17855MCM AAA-lid domain (MCM_lid)MCM AAA-lid domainThis entry represents the AAA-lid domain found in MCM proteins.Domain
D [auth 5]PF17207MCM OB domain (MCM_OB)MCM OB domainThis family contains an OB-fold found within MCM proteins. This domain contains an insertion at the zinc binding motif [2].Domain
E [auth 6]PF00493MCM P-loop domain (MCM)MCM P-loop domain- Domain
E [auth 6]PF14551MCM N-terminal domain (MCM_N)MCM N-terminal domainThis family contains the N-terminal domain of MCM proteins.Domain
E [auth 6]PF17855MCM AAA-lid domain (MCM_lid)MCM AAA-lid domainThis entry represents the AAA-lid domain found in MCM proteins.Domain
E [auth 6]PF17207MCM OB domain (MCM_OB)MCM OB domainThis family contains an OB-fold found within MCM proteins. This domain contains an insertion at the zinc binding motif [2].Domain
G [auth 8]PF22912Zinc finger domain of DNA polymerase-epsilon (zf-DPOE)Zinc finger domain of DNA polymerase-epsilonThis zinc finger domain is found in the epsilon subunit of DNA polymerase.Domain
G [auth 8]PF08490Domain of unknown function (DUF1744) (DUF1744)Domain of unknown function (DUF1744)This domain is found at the C-terminal of the epsilon catalytic subunit of DNA polymerase. It is found C terminal to Pfam:PF03104 and Pfam:PF00136.Domain
H [auth 9]PF04042DNA polymerase alpha/epsilon subunit B (DNA_pol_E_B)DNA polymerase alpha/epsilon subunit B- Family
I [auth A]PF05916GINS complex protein helical bundle domain (Sld5)GINS complex protein helical bundle domainThis entry represents the C-terminal alpha helical bundle domain. The eukaryotic GINS complex is essential for the initiation and elongation phases of DNA replication [1-3]. It consists of four paralogous protein subunits (Sld5, Psf1, Psf2 and Psf3) ...This entry represents the C-terminal alpha helical bundle domain. The eukaryotic GINS complex is essential for the initiation and elongation phases of DNA replication [1-3]. It consists of four paralogous protein subunits (Sld5, Psf1, Psf2 and Psf3), all of which are included in this family. The GINS complex is conserved from yeast to humans, and has been shown in human to bind directly to DNA primase [4].
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth 2]DNA replication licensing factor MCM2---
J [auth B]DNA replication complex GINS protein PSF2---
K [auth C]DNA replication complex GINS protein PSF3-
L [auth D]DNA replication complex GINS protein SLD5-
M [auth E]Cell division control protein 45
N [auth F],
O [auth G],
P [auth H]		DNA polymerase alpha-binding protein
Q [auth I]Topoisomerase 1-associated factor 1
R [auth J]Chromosome segregation in meiosis protein 3
S [auth K]Mediator of replication checkpoint protein 1
T [auth L]FACT complex subunit SPT16-
U [auth M]FACT complex subunit POB3
B [auth 3]DNA replication licensing factor MCM3
V [auth N],
Z [auth R]		Histone H3---
AA [auth S],
W [auth O]		Histone H4
X [auth P]Histone H2A.1
Y [auth Q]Histone H2B.2
BA [auth X]DNA (51-MER)---
CA [auth Y]DNA (39-MER)---
C [auth 4]DNA replication licensing factor MCM4
D [auth 5]Minichromosome maintenance protein 5
E [auth 6]DNA replication licensing factor MCM6
F [auth 7]DNA replication licensing factor MCM7---
G [auth 8]DNA polymerase epsilon catalytic subunit A
H [auth 9]DNA polymerase epsilon subunit B
I [auth A]DNA replication complex GINS protein PSF1-

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
K [auth C]IPR036224GINS, helical bundle-like domain superfamilyHomologous Superfamily
K [auth C]IPR021151GINS subunit, domain ADomain
K [auth C]IPR010492GINS complex, subunit Psf3Family
K [auth C]IPR038437GINS complex, subunit Psf3 superfamilyHomologous Superfamily
L [auth D]IPR008591GINS complex subunit Sld5Family
L [auth D]IPR038749GINS complex protein Sld5, alpha-helical domainDomain
L [auth D]IPR036224GINS, helical bundle-like domain superfamilyHomologous Superfamily
L [auth D]IPR021151GINS subunit, domain ADomain
L [auth D]IPR031633DNA replication complex GINS protein SLD5, C-terminalDomain
M [auth E]IPR003874CDC45 familyFamily
N [auth F],
O [auth G],
P [auth H]		IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
N [auth F],
O [auth G],
P [auth H]		IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
N [auth F],
O [auth G],
P [auth H]		IPR022100Minichromosome loss protein Mcl1, middle regionDomain
N [auth F],
O [auth G],
P [auth H]		IPR048591DNA polymerase alpha-binding protein Ctf4-like, C-terminal domainDomain
Q [auth I]IPR044998TimelessFamily
Q [auth I]IPR006906Timeless, N-terminalDomain
R [auth J]IPR012923Chromosome segregation in meiosis protein 3Domain
R [auth J]IPR040038TIPIN/Csm3/Swi3Family
S [auth K]IPR024146ClaspinFamily
S [auth K]IPR018564DNA replication checkpoint mediator, MRC1 domainDomain
T [auth L]IPR033825FACT complex subunit Spt16, peptidase M24-like domainDomain
T [auth L]IPR048969FACT complex subunit SPT16, C-terminal domainDomain
T [auth L]IPR029149Creatinase/Aminopeptidase P/Spt16, N-terminalHomologous Superfamily
T [auth L]IPR011993PH-like domain superfamilyHomologous Superfamily
T [auth L]IPR013719Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domainDomain
T [auth L]IPR040258FACT complex subunit Spt16Family
T [auth L]IPR029148FACT complex subunit Spt16, N-terminal lobe domainDomain
T [auth L]IPR013953FACT complex subunit Spt16 domainDomain
T [auth L]IPR036005Creatinase/aminopeptidase-likeHomologous Superfamily
T [auth L]IPR000994Peptidase M24Domain
U [auth M]IPR038167SSRP1 domain superfamilyHomologous Superfamily
U [auth M]IPR050454RTT106/SSRP1 Histone Chaperone/FACT ComplexFamily
U [auth M]IPR035417FACT complex subunit SSRP1/POB3, N-terminal PH domainDomain
U [auth M]IPR000969FACT complex subunit SSRP1/POB3Family
U [auth M]IPR011993PH-like domain superfamilyHomologous Superfamily
U [auth M]IPR013719Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domainDomain
U [auth M]IPR048993FACT complex subunit SSRP1-like, first PH domainDomain
U [auth M]IPR024954SSRP1, dimerization domainDomain
B [auth 3]IPR031327Mini-chromosome maintenance proteinFamily
B [auth 3]IPR018525Mini-chromosome maintenance, conserved siteConserved Site
B [auth 3]IPR003593AAA+ ATPase domainDomain
B [auth 3]IPR001208MCM domainDomain
B [auth 3]IPR041562MCM, AAA-lid domainDomain
B [auth 3]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
B [auth 3]IPR027925MCM, N-terminal domainDomain
B [auth 3]IPR008046DNA replication licensing factor Mcm3Family
B [auth 3]IPR033762MCM OB domainDomain
B [auth 3]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
AA [auth S],
W [auth O]		IPR009072Histone-foldHomologous Superfamily
AA [auth S],
W [auth O]		IPR035425CENP-T/Histone H4, histone foldDomain
AA [auth S],
W [auth O]		IPR001951Histone H4Family
AA [auth S],
W [auth O]		IPR019809Histone H4, conserved siteConserved Site
X [auth P]IPR009072Histone-foldHomologous Superfamily
X [auth P]IPR007125Histone H2A/H2B/H3Domain
X [auth P]IPR002119Histone H2AFamily
X [auth P]IPR032454Histone H2A, C-terminal domainDomain
X [auth P]IPR032458Histone H2A conserved siteConserved Site
Y [auth Q]IPR009072Histone-foldHomologous Superfamily
Y [auth Q]IPR007125Histone H2A/H2B/H3Domain
Y [auth Q]IPR000558Histone H2BFamily
C [auth 4]IPR031327Mini-chromosome maintenance proteinFamily
C [auth 4]IPR018525Mini-chromosome maintenance, conserved siteConserved Site
C [auth 4]IPR001208MCM domainDomain
C [auth 4]IPR041562MCM, AAA-lid domainDomain
C [auth 4]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
C [auth 4]IPR027925MCM, N-terminal domainDomain
C [auth 4]IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
C [auth 4]IPR008047Mini-chromosome maintenance complex protein 4Family
C [auth 4]IPR033762MCM OB domainDomain
C [auth 4]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
D [auth 5]IPR031327Mini-chromosome maintenance proteinFamily
D [auth 5]IPR018525Mini-chromosome maintenance, conserved siteConserved Site
D [auth 5]IPR001208MCM domainDomain
D [auth 5]IPR041562MCM, AAA-lid domainDomain
D [auth 5]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
D [auth 5]IPR027925MCM, N-terminal domainDomain
D [auth 5]IPR033762MCM OB domainDomain
D [auth 5]IPR008048DNA replication licensing factor Mcm5Family
D [auth 5]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
E [auth 6]IPR008049DNA replication licensing factor Mcm6Family
E [auth 6]IPR041024Mcm6, C-terminal winged-helix domainDomain
E [auth 6]IPR031327Mini-chromosome maintenance proteinFamily
E [auth 6]IPR018525Mini-chromosome maintenance, conserved siteConserved Site
E [auth 6]IPR001208MCM domainDomain
E [auth 6]IPR041562MCM, AAA-lid domainDomain
E [auth 6]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
E [auth 6]IPR027925MCM, N-terminal domainDomain
E [auth 6]IPR033762MCM OB domainDomain
E [auth 6]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
G [auth 8]IPR036397Ribonuclease H superfamilyHomologous Superfamily
G [auth 8]IPR006134DNA-directed DNA polymerase, family B, multifunctional domainDomain
G [auth 8]IPR012337Ribonuclease H-like superfamilyHomologous Superfamily
G [auth 8]IPR023211DNA polymerase, palm domain superfamilyHomologous Superfamily
G [auth 8]IPR006172DNA-directed DNA polymerase, family BFamily
G [auth 8]IPR029703DNA polymerase epsilon catalytic subunitFamily
G [auth 8]IPR043502DNA/RNA polymerase superfamilyHomologous Superfamily
G [auth 8]IPR013697DNA polymerase epsilon, catalytic subunit A, C-terminalDomain
G [auth 8]IPR006133DNA-directed DNA polymerase, family B, exonuclease domainDomain
G [auth 8]IPR042087DNA polymerase family B, thumb domainHomologous Superfamily
H [auth 9]IPR016266DNA polymerase epsilon, subunit BFamily
H [auth 9]IPR007185DNA polymerase alpha/delta/epsilon, subunit BDomain
I [auth A]IPR005339GINS complex, subunit Psf1Family
I [auth A]IPR036224GINS, helical bundle-like domain superfamilyHomologous Superfamily
I [auth A]IPR021151GINS subunit, domain ADomain