12DL | pdb_000012dl

Native structure of the cytoplasmic lattice (CPL) asymmetric unit from mouse MII eggs

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
H [auth LA]SCOP2B SuperfamilyEukaryotic type KH-domain (KH-domain type I) 8052235 3001023 SCOP2B (2022-06-29)
X [auth BB]SCOP2B SuperfamilyPUA domain-like 8038600 3001015 SCOP2B (2022-06-29)
W [auth BA]SCOP2B SuperfamilyPUA domain-like 8038600 3001015 SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
T [auth EA]PF00091Tubulin/FtsZ family, GTPase domain (Tubulin)Tubulin/FtsZ family, GTPase domainThis family includes the tubulin alpha, beta and gamma chains, as well as the bacterial FtsZ family of proteins. Members of this family are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ...This family includes the tubulin alpha, beta and gamma chains, as well as the bacterial FtsZ family of proteins. Members of this family are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ and tubulin are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tubulin is the major component of microtubules.
Domain
T [auth EA]PF03953Tubulin C-terminal domain (Tubulin_C)Tubulin C-terminal domainThis family includes the tubulin alpha, beta and gamma chains. Members of this family are involved in polymer formation. Tubulins are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tub ...This family includes the tubulin alpha, beta and gamma chains. Members of this family are involved in polymer formation. Tubulins are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tubulin is the major component of microtubules. (The FtsZ GTPases have been split into their won family).
Domain
PF08527Protein-arginine deiminase (PAD) middle domain (PAD_M)Protein-arginine deiminase (PAD) middle domainThis family represents the central non-catalytic domain of protein-arginine deiminase. This domain has an immunoglobulin-like fold. Domain
PF03068Protein-arginine deiminase (PAD) (PAD)Protein-arginine deiminase (PAD)- Family
I [auth MA]PF05729NACHT domain (NACHT)NACHT domainThis NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation [1]. This family is closely related to Pfam:PF00931. Domain
I [auth MA]PF13516Leucine Rich repeat (LRR_6)Leucine Rich repeat- Repeat
I [auth MA]PF02758PAAD/DAPIN/Pyrin domain (PYRIN)PAAD/DAPIN/Pyrin domainThis domain is predicted to contain 6 alpha helices and to have the same fold as the Pfam:PF00531 domain. This similarity may mean that this is a protein-protein interaction domain. Domain
I [auth MA]PF17776NLRC4 helical domain HD2 (NLRC4_HD2)NLRC4 helical domain HD2This entry represents a helical domain found in the NLRC4 protein [2] and NOD2 protein [1]. Domain
I [auth MA]PF17779NOD2 winged helix domain (WHD_NOD2)NOD2 winged helix domainThis winged helix domain is found in the NOD2 protein [1]. Its molecular function is not known. Domain
H [auth LA]PF16005KH-like RNA-binding domain (MOEP19)KH-like RNA-binding domainMOEP19 is a family of mammalian KH-like RNA-binding motifs. The family is expressed during early embryogenesis. It appears to effect an early form of molecular asymmetry within the murine oocyte cytoplasm. The family marks a defined cortical cytoplas ...MOEP19 is a family of mammalian KH-like RNA-binding motifs. The family is expressed during early embryogenesis. It appears to effect an early form of molecular asymmetry within the murine oocyte cytoplasm. The family marks a defined cortical cytoplasmic domain in oocytes and provides evidence for mammalian oocyte polarity and a form of pre-patterning that persists in zygotes and early embryos through the morula stage [1].
Domain
D [auth IA],
GA [auth JA]		PF16005KH-like RNA-binding domain (MOEP19)KH-like RNA-binding domainMOEP19 is a family of mammalian KH-like RNA-binding motifs. The family is expressed during early embryogenesis. It appears to effect an early form of molecular asymmetry within the murine oocyte cytoplasm. The family marks a defined cortical cytoplas ...MOEP19 is a family of mammalian KH-like RNA-binding motifs. The family is expressed during early embryogenesis. It appears to effect an early form of molecular asymmetry within the murine oocyte cytoplasm. The family marks a defined cortical cytoplasmic domain in oocytes and provides evidence for mammalian oocyte polarity and a form of pre-patterning that persists in zygotes and early embryos through the morula stage [1].
Domain
B [auth GB],
C [auth GA]		PF05729NACHT domain (NACHT)NACHT domainThis NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation [1]. This family is closely related to Pfam:PF00931. Domain
B [auth GB],
C [auth GA]		PF13516Leucine Rich repeat (LRR_6)Leucine Rich repeat- Repeat
B [auth GB],
C [auth GA]		PF17776NLRC4 helical domain HD2 (NLRC4_HD2)NLRC4 helical domain HD2This entry represents a helical domain found in the NLRC4 protein [2] and NOD2 protein [1]. Domain
B [auth GB],
C [auth GA]		PF17779NOD2 winged helix domain (WHD_NOD2)NOD2 winged helix domainThis winged helix domain is found in the NOD2 protein [1]. Its molecular function is not known. Domain
FA [auth PA]PF12937F-box-like (F-box-like)F-box-likeThis is an F-box-like family. Domain
BA [auth QB],
CA [auth QA],
EA [auth QC]		PF03931Skp1 family, tetramerisation domain (Skp1_POZ)Skp1 family, tetramerisation domainDomain
BA [auth QB],
CA [auth QA],
EA [auth QC]		PF01466Skp1 family, dimerisation domain (Skp1)Skp1 family, dimerisation domainDomain
AA [auth OA]PF12937F-box-like (F-box-like)F-box-likeThis is an F-box-like family. Domain
Y [auth CA],
Z [auth CB]		PF00179Ubiquitin-conjugating enzyme (UQ_con)Ubiquitin-conjugating enzymeProteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cystein ...Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine [4, 5].
Domain
W [auth BA],
X [auth BB]		PF12148Tandem tudor domain within UHRF1 (TTD)Tandem tudor domain within UHRF1TTD, tandem tudor domain within UHRF1 preferentially binds H3 histone tails trimethylated at Lys-9. It specifically recognises H3 tail peptides with the heterochromatin-associated modification state of trimethylated lysine 9 and unmodified lysine 4 ( ...TTD, tandem tudor domain within UHRF1 preferentially binds H3 histone tails trimethylated at Lys-9. It specifically recognises H3 tail peptides with the heterochromatin-associated modification state of trimethylated lysine 9 and unmodified lysine 4 (H3K4me0/K9me3). This domain is found in eukaryotes and is found in association with Pfam:PF00097, Pfam:PF02182, Pfam:PF00628, Pfam:PF00240.
Domain
W [auth BA],
X [auth BB]		PF02182SAD/SRA domain (SAD_SRA)SAD/SRA domainThe domain goes by several names including SAD [1], SRA [2] and YDG [3]. It adopts a beta barrel, modified PUA-like, fold that is widely present in eukaryotic chromatin proteins and in bacteria [4]. Versions of this domain are known to bind hemi-me ...The domain goes by several names including SAD [1], SRA [2] and YDG [3]. It adopts a beta barrel, modified PUA-like, fold that is widely present in eukaryotic chromatin proteins and in bacteria [4]. Versions of this domain are known to bind hemi-methylated CpG dinucleotides and also other 5mC containing dinucleotides. The domain binds DNA by flipping out the methylated cytosine base from the DNA double helix [5].The conserved tyrosine and aspartate residues and a glycine rich patch are critical for recognition of the flipped out base [4][5]. Mammalian UHRF1 that contains this domain plays an important role in maintenance of methylation at CpG dinucleotides by recruiting DNMT1 to hemimethylated sites associated with replication forks [2]. The SAD/SRA domain has been combined with other domains involved in the ubiquitin pathway on multiple occasions and such proteins link recognition of DNA methylation to chromatin-protein ubiquitination [4]. The domain is also found in species that lack DNA methylation, such as certain apicomplexans, suggestive of other DNA-binding modes or functions [4]. A highly derived and distinct version of the domain is also found in fungi where it is fused to AlkB-type 2OGFeDO domains [6]. In bacteria, the domain is usually fused or associated with restriction endonucleases, many of which target methylated or hemi-methylated DNA [4].
Domain
W [auth BA],
X [auth BB]		PF00628PHD-finger (PHD)PHD-fingerPHD 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
W [auth BA],
X [auth BB]		PF00240Ubiquitin family (ubiquitin)Ubiquitin familyThis family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].
Domain
U [auth DA],
V [auth DB]		PF05729NACHT domain (NACHT)NACHT domainThis NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation [1]. This family is closely related to Pfam:PF00931. Domain
U [auth DA],
V [auth DB]		PF13516Leucine Rich repeat (LRR_6)Leucine Rich repeat- Repeat
U [auth DA],
V [auth DB]		PF17776NLRC4 helical domain HD2 (NLRC4_HD2)NLRC4 helical domain HD2This entry represents a helical domain found in the NLRC4 protein [2] and NOD2 protein [1]. Domain
U [auth DA],
V [auth DB]		PF17779NOD2 winged helix domain (WHD_NOD2)NOD2 winged helix domainThis winged helix domain is found in the NOD2 protein [1]. Its molecular function is not known. Domain
A [auth FA]PF00091Tubulin/FtsZ family, GTPase domain (Tubulin)Tubulin/FtsZ family, GTPase domainThis family includes the tubulin alpha, beta and gamma chains, as well as the bacterial FtsZ family of proteins. Members of this family are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ...This family includes the tubulin alpha, beta and gamma chains, as well as the bacterial FtsZ family of proteins. Members of this family are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ and tubulin are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tubulin is the major component of microtubules.
Domain
A [auth FA]PF03953Tubulin C-terminal domain (Tubulin_C)Tubulin C-terminal domainThis family includes the tubulin alpha, beta and gamma chains. Members of this family are involved in polymer formation. Tubulins are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tub ...This family includes the tubulin alpha, beta and gamma chains. Members of this family are involved in polymer formation. Tubulins are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tubulin is the major component of microtubules. (The FtsZ GTPases have been split into their won family).
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
T [auth EA]Tubulin alpha-1C chain
Inactive protein-arginine deiminase type-6
I [auth MA]NLR family, pyrin domain containing 4F - -
H [auth LA]KH domain-containing protein 3
G [auth KA]Zinc finger BED domain-containing protein 3
E [auth HB],
F [auth HA]		Transducin-like enhancer protein 6
D [auth IA],
GA [auth JA]		Oocyte-expressed protein homolog
B [auth GB],
C [auth GA]		NACHT, LRR and PYD domains-containing protein 5
FA [auth PA]F-box and WD-40 domain protein 21- -
DA [auth NA]Expressed sequence C85627- -
BA [auth QB],
CA [auth QA],
EA [auth QC]		S-phase kinase-associated protein 1
AA [auth OA]F-box and WD-40 domain protein 19- -
Y [auth CA],
Z [auth CB]		Ubiquitin-conjugating enzyme E2 D3
W [auth BA],
X [auth BB]		E3 ubiquitin-protein ligase UHRF1
U [auth DA],
V [auth DB]		NACHT, LRR and PYD domains-containing protein 14
A [auth FA]Tubulin beta-4B chain

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
T [auth EA]IPR003008Tubulin/FtsZ, GTPase domainDomain
T [auth EA]IPR008280Tubulin/FtsZ, C-terminalHomologous Superfamily
T [auth EA]IPR037103Tubulin/FtsZ-like, C-terminal domainHomologous Superfamily
T [auth EA]IPR017975Tubulin, conserved siteConserved Site
T [auth EA]IPR002452Alpha tubulinFamily
T [auth EA]IPR000217TubulinFamily
T [auth EA]IPR023123Tubulin, C-terminalHomologous Superfamily
T [auth EA]IPR018316Tubulin/FtsZ, 2-layer sandwich domainDomain
T [auth EA]IPR036525Tubulin/FtsZ, GTPase domain superfamilyHomologous Superfamily
IPR013732Protein-arginine deiminase (PAD), N-terminalDomain
IPR013733Protein-arginine deiminase (PAD), central domainDomain
IPR008972CupredoxinHomologous Superfamily
IPR038685PAD, N-terminal domain superfamilyHomologous Superfamily
IPR013530Protein-arginine deiminase, C-terminalDomain
IPR036556Protein-arginine deiminase, central domain superfamilyHomologous Superfamily
IPR004303Protein-arginine deiminaseFamily
I [auth MA]IPR011029Death-like domain superfamilyHomologous Superfamily
I [auth MA]IPR032675Leucine-rich repeat domain superfamilyHomologous Superfamily
I [auth MA]IPR041267NACHT, LRR and PYD domains-containing protein, helical domain HD2Domain
I [auth MA]IPR050637NLRP family, innate immunity and inflammation regulatorsFamily
I [auth MA]IPR001611Leucine-rich repeatRepeat
I [auth MA]IPR004020DAPIN domainDomain
I [auth MA]IPR041075NOD1/2, winged helix domainDomain
I [auth MA]IPR007111NACHT nucleoside triphosphataseDomain
I [auth MA]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
H [auth LA]IPR036612K Homology domain, type 1 superfamilyHomologous Superfamily
H [auth LA]IPR051778KH Domain-Containing Protein 1Family
H [auth LA]IPR031952KH-like RNA-binding domainDomain
G [auth KA]IPR036236Zinc finger C2H2 superfamilyHomologous Superfamily
G [auth KA]IPR043471Zinc finger BED domain-containing protein 2/3Family
E [auth HB],
F [auth HA]		IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
E [auth HB],
F [auth HA]		IPR009146Groucho/transducin-like enhancerFamily
E [auth HB],
F [auth HA]		IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
E [auth HB],
F [auth HA]		IPR001680WD40 repeatRepeat
D [auth IA],
GA [auth JA]		IPR036612K Homology domain, type 1 superfamilyHomologous Superfamily
D [auth IA],
GA [auth JA]		IPR051778KH Domain-Containing Protein 1Family
D [auth IA],
GA [auth JA]		IPR031952KH-like RNA-binding domainDomain
B [auth GB],
C [auth GA]		IPR007111NACHT nucleoside triphosphataseDomain
B [auth GB],
C [auth GA]		IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
B [auth GB],
C [auth GA]		IPR041267NACHT, LRR and PYD domains-containing protein, helical domain HD2Domain
B [auth GB],
C [auth GA]		IPR001611Leucine-rich repeatRepeat
B [auth GB],
C [auth GA]		IPR041075NOD1/2, winged helix domainDomain
B [auth GB],
C [auth GA]		IPR032675Leucine-rich repeat domain superfamilyHomologous Superfamily
B [auth GB],
C [auth GA]		IPR050637NLRP family, innate immunity and inflammation regulatorsFamily
FA [auth PA]IPR036047F-box-like domain superfamilyHomologous Superfamily
FA [auth PA]IPR001810F-box domainDomain
FA [auth PA]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
FA [auth PA]IPR052121F-box Protein Family Substrate Recognition ComponentsFamily
FA [auth PA]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
DA [auth NA]IPR036047F-box-like domain superfamilyHomologous Superfamily
DA [auth NA]IPR001810F-box domainDomain
DA [auth NA]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
DA [auth NA]IPR052121F-box Protein Family Substrate Recognition ComponentsFamily
BA [auth QB],
CA [auth QA],
EA [auth QC]		IPR016073SKP1 component, POZ domainDomain
BA [auth QB],
CA [auth QA],
EA [auth QC]		IPR001232S-phase kinase-associated protein 1-likeFamily
BA [auth QB],
CA [auth QA],
EA [auth QC]		IPR036296SKP1-like, dimerisation domain superfamilyHomologous Superfamily
BA [auth QB],
CA [auth QA],
EA [auth QC]		IPR016072SKP1 component, dimerisationDomain
BA [auth QB],
CA [auth QA],
EA [auth QC]		IPR011333SKP1/BTB/POZ domain superfamilyHomologous Superfamily
BA [auth QB],
CA [auth QA],
EA [auth QC]		IPR016897S-phase kinase-associated protein 1Family
AA [auth OA]IPR036047F-box-like domain superfamilyHomologous Superfamily
AA [auth OA]IPR001810F-box domainDomain
AA [auth OA]IPR052121F-box Protein Family Substrate Recognition ComponentsFamily
AA [auth OA]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
Y [auth CA],
Z [auth CB]		IPR016135Ubiquitin-conjugating enzyme/RWD-likeHomologous Superfamily
Y [auth CA],
Z [auth CB]		IPR000608Ubiquitin-conjugating (UBC), catalytic core domainDomain
Y [auth CA],
Z [auth CB]		IPR023313Ubiquitin-conjugating enzyme, active siteActive Site
W [auth BA],
X [auth BB]		IPR015947PUA-like superfamilyHomologous Superfamily
W [auth BA],
X [auth BB]		IPR001965Zinc finger, PHD-typeDomain
W [auth BA],
X [auth BB]		IPR047406E3 ubiquitin-protein ligase UHRF1, ubiquitin-like domainDomain
W [auth BA],
X [auth BB]		IPR013083Zinc finger, RING/FYVE/PHD-typeHomologous Superfamily
W [auth BA],
X [auth BB]		IPR001841Zinc finger, RING-typeDomain
W [auth BA],
X [auth BB]		IPR036987SRA-YDG superfamilyHomologous Superfamily
W [auth BA],
X [auth BB]		IPR003105SRA-YDGDomain
W [auth BA],
X [auth BB]		IPR019787Zinc finger, PHD-fingerDomain
W [auth BA],
X [auth BB]		IPR011011Zinc finger, FYVE/PHD-typeHomologous Superfamily
W [auth BA],
X [auth BB]		IPR017907Zinc finger, RING-type, conserved siteConserved Site
W [auth BA],
X [auth BB]		IPR000626Ubiquitin-like domainDomain
W [auth BA],
X [auth BB]		IPR021991UHRF1, tandem tudor domainDomain
W [auth BA],
X [auth BB]		IPR029071Ubiquitin-like domain superfamilyHomologous Superfamily
W [auth BA],
X [auth BB]		IPR045134UHRF1/2-likeFamily
U [auth DA],
V [auth DB]		IPR032675Leucine-rich repeat domain superfamilyHomologous Superfamily
U [auth DA],
V [auth DB]		IPR041267NACHT, LRR and PYD domains-containing protein, helical domain HD2Domain
U [auth DA],
V [auth DB]		IPR050637NLRP family, innate immunity and inflammation regulatorsFamily
U [auth DA],
V [auth DB]		IPR001611Leucine-rich repeatRepeat
U [auth DA],
V [auth DB]		IPR041075NOD1/2, winged helix domainDomain
U [auth DA],
V [auth DB]		IPR007111NACHT nucleoside triphosphataseDomain
U [auth DA],
V [auth DB]		IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
A [auth FA]IPR008280Tubulin/FtsZ, C-terminalHomologous Superfamily
A [auth FA]IPR017975Tubulin, conserved siteConserved Site
A [auth FA]IPR023123Tubulin, C-terminalHomologous Superfamily
A [auth FA]IPR002453Beta tubulinFamily
A [auth FA]IPR013838Beta tubulin, autoregulation binding siteBinding Site
A [auth FA]IPR018316Tubulin/FtsZ, 2-layer sandwich domainDomain
A [auth FA]IPR003008Tubulin/FtsZ, GTPase domainDomain
A [auth FA]IPR037103Tubulin/FtsZ-like, C-terminal domainHomologous Superfamily
A [auth FA]IPR000217TubulinFamily
A [auth FA]IPR036525Tubulin/FtsZ, GTPase domain superfamilyHomologous Superfamily