9YGY | pdb_00009ygy

Structure of a GRP94 folding intermediate engaged with a CCDC134- and FKBP11-bound secretory translocon


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
G [auth D]SCOP2B SuperfamilySecY-like 8098818 3000333 SCOP2B (2022-06-29)
I [auth F]SCOP2B SuperfamilyProtein translocase subunit SecE-like 8098782 3002174 SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
G [auth D]PF10559Plug domain of Sec61p (Plug_translocon)Plug domain of Sec61pThe Sec61/SecY translocon mediates translocation of proteins across the membrane and integration of membrane proteins into the lipid bilayer. The structure of the translocon revealed a plug domain blocking the pore on the lumenal side.The plug is unl ...The Sec61/SecY translocon mediates translocation of proteins across the membrane and integration of membrane proteins into the lipid bilayer. The structure of the translocon revealed a plug domain blocking the pore on the lumenal side.The plug is unlikely to be important for sealing the translocation pore in yeast but it plays a role in stabilising Sec61p during translocon formation. The domain runs from residues 52-74 [1].
Domain
G [auth D]PF00344SecY (SecY)SecY- Family
K [auth I]PF02516Oligosaccharyl transferase STT3, N-terminal (STT3)Oligosaccharyl transferase STT3, N-terminalThis entry consists of the oligosaccharyl transferase STT3 subunit and related proteins. The STT3 subunit is part of the oligosaccharyl transferase (OTase) complex of proteins and is required for its activity [2]. In eukaryotes, OTase transfers a l ...This entry consists of the oligosaccharyl transferase STT3 subunit and related proteins. The STT3 subunit is part of the oligosaccharyl transferase (OTase) complex of proteins and is required for its activity [2]. In eukaryotes, OTase transfers a lipid-linked core-oligosaccharide to selected asparagine residues in the ER [2]. In the archaea STT3 occurs alone, rather than in an OTase complex, and is required for N-glycosylation of asparagines [3-4]. This entry represents the N-terminal domain, consisting of transmembrane helices.
Domain
K [auth I]PF22627AglB core domain (AglB_core-like)AglB core domainThis entry represents the C-terminal core domain of archaeal oligosaccharyltransferase AglB that transfers oligosaccharide chain from a lipid-linked oligosaccharide (LLO) donor to the asparagine residues in the N-glycosylation sequon, Asn-X-Ser/Thr ( ...This entry represents the C-terminal core domain of archaeal oligosaccharyltransferase AglB that transfers oligosaccharide chain from a lipid-linked oligosaccharide (LLO) donor to the asparagine residues in the N-glycosylation sequon, Asn-X-Ser/Thr (X=Pro) [1-5]. In the archaea AlgB, it occurs alone, rather than in complex as the eukaryotic homologue STT3. This domain adopts a mixed alpha/beta fold and contains a highly conserved WWDYG motif that may be of functional relevance.
Domain
O [auth M2]PF02109DAD family (DAD)DAD family- Family
Q [auth N2]PF23358OST48 middle domain (OST48_MD)OST48 middle domainThis entry represents the middle domain (MD) of OST48 from animals and its orthologue from yeast Wbp1 [1,2]. OST48/Wbp1 is a subunit of the oligosaccharyl transferase (OST) complex that catalyses the initial transfer of a defined glycan (Glc3Man9GlcN ...This entry represents the middle domain (MD) of OST48 from animals and its orthologue from yeast Wbp1 [1,2]. OST48/Wbp1 is a subunit of the oligosaccharyl transferase (OST) complex that catalyses the initial transfer of a defined glycan (Glc3Man9GlcNAc2 in eukaryotes) from the lipid carrier dolichol-pyrophosphate to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains, the first step in protein N-glycosylation [1,2]. This domain adopts a beta-sandwich fold, which together with the N-terminal domain (Pfam:PF03345), interacts with riphophorin II/Swp1 subunit [3].
Domain
Q [auth N2]PF03345OST48, N-terminal domain (OST48_N)OST48, N-terminal domainMembers of this entry are involved in asparagine-linked protein glycosylation. In particular, dolichyl-diphosphooligosaccharide-protein glycosyltransferase (DDOST), also known as oligosaccharyltransferase, transfers the high-mannose sugar GlcNAc(2)-M ...Members of this entry are involved in asparagine-linked protein glycosylation. In particular, dolichyl-diphosphooligosaccharide-protein glycosyltransferase (DDOST), also known as oligosaccharyltransferase, transfers the high-mannose sugar GlcNAc(2)-Man(9)-Glc(3) from a dolichol-linked donor to an asparagine acceptor in a consensus Asn-X-Ser/Thr motif. In most eukaryotes, the DDOST complex is composed of three subunits, which in humans are described as a 48kD subunit, ribophorin I, and ribophorin II. However, the yeast DDOST appears to consist of six subunits (alpha, beta, gamma, delta, epsilon, zeta). The yeast beta subunit is a 45kD polypeptide, previously discovered as the Wbp1 protein, with known sequence similarity to the human 48kD subunit and the other orthologues. This is the N-terminal domain of OST48 subunits from animals and plants and the orthologue from yeast Wbp1. This domain is distantly related to the IFT52 N-terminal domain (Pfam:PF23355).
Domain
R [auth O2]PF04597Ribophorin I (Ribophorin_I)Ribophorin I- Family
I [auth F]PF00584SecE/Sec61-gamma subunits of protein translocation complex (SecE)SecE/Sec61-gamma subunits of protein translocation complex- Family
E [auth A]PF00254FKBP-type peptidyl-prolyl cis-trans isomerase (FKBP_C)FKBP-type peptidyl-prolyl cis-trans isomeraseDomain
C [auth 7]PF07074Translocon-associated protein, gamma subunit (TRAP-gamma) (TRAP-gamma)Translocon-associated protein, gamma subunit (TRAP-gamma)- Family
S [auth P2]PF05817Ribophorin II N-terminal domain (Ribophorin_II)Ribophorin II N-terminal domain- Repeat
S [auth P2]PF23861Ribophorin II second domain (Ribophorin_II_2nd)Ribophorin II second domainThis entry represents the second beta sandwich domain found in eukaryotic Ribophorin II (RPN2) proteins. The mammalian oligosaccharyltransferase (OST) is a protein complex that effects the cotranslational N-glycosylation of newly synthesised polypept ...This entry represents the second beta sandwich domain found in eukaryotic Ribophorin II (RPN2) proteins. The mammalian oligosaccharyltransferase (OST) is a protein complex that effects the cotranslational N-glycosylation of newly synthesised polypeptides, and is composed of the following proteins: ribophorins I and II (RI and RII), OST48, and Dadl, N33/IAP, OST4, STT3. The family also includes the SWP1 protein from yeast. In yeast the oligosaccharyltransferase complex is composed 7 or 8 subunits, SWP1, being one of them [2][3].
Domain
S [auth P2]PF25147Ribophorin_II, C-terminal domain (Ribophorin_II_C)Ribophorin_II, C-terminal domainThis domain is found at the C-terminal of human Ribophorin II, a subunit of the oligosaccharyl transferase (OST) complex that catalyses the first step in protein N-glycosylation. This domain shows an all-alpha configuration and is often found associa ...This domain is found at the C-terminal of human Ribophorin II, a subunit of the oligosaccharyl transferase (OST) complex that catalyses the first step in protein N-glycosylation. This domain shows an all-alpha configuration and is often found associated to Pfam:PF05817, Pfam:PF23861 and Pfam:PF23860.
Domain
S [auth P2]PF23860Ribophorin II third domain (Ribophorin_II_3rd)Ribophorin II third domainThis entry represents the third domain of eukaryotic Ribophorin II (RPN2) proteins. The mammalian oligosaccharyltransferase (OST) is a protein complex that effects the cotranslational N-glycosylation of newly synthesised polypeptides, and is composed ...This entry represents the third domain of eukaryotic Ribophorin II (RPN2) proteins. The mammalian oligosaccharyltransferase (OST) is a protein complex that effects the cotranslational N-glycosylation of newly synthesised polypeptides, and is composed of the following proteins: ribophorins I and II (RI and RII), OST48, and Dadl, N33/IAP, OST4, STT3. The family also includes the SWP1 protein from yeast. In yeast the oligosaccharyltransferase complex is composed 7 or 8 subunits, SWP1, being one of them [2][3].
Domain
P [auth N]PF09775Keratinocyte-associated protein 2 (Keratin_assoc)Keratinocyte-associated protein 2- Family
N [auth L2]PF05251Oligosaccharyltransferase subunit 5 (Ost5)Oligosaccharyltransferase subunit 5- Family
M [auth K2]PF10215Oligosaccaryltransferase (Ost4)Oligosaccaryltransferase- Family
L [auth J]PF04756OST3 / OST6 family, transporter family (OST3_OST6)OST3 / OST6 family, transporter family- Family
J [auth G]PF06624Ribosome associated membrane protein RAMP4 (RAMP4)Ribosome associated membrane protein RAMP4- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
B [auth 6]Translocon-associated protein subunit beta-
D [auth 8]Translocon-associated protein subunit delta- -
G [auth D]Protein transport protein Sec61 subunit alpha isoform 1
K [auth I]Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A
O [auth M2]Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1
Q [auth N2]Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit
R [auth O2]Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1
T [auth y3]Endoplasmin
I [auth F]Protein transport protein Sec61 subunit gamma
H [auth E]Protein transport protein Sec61 subunit beta
F [auth B]Coiled-coil domain-containing protein 134
E [auth A]Peptidyl-prolyl cis-trans isomerase FKBP11 -
C [auth 7]Translocon-associated protein subunit gamma-
S [auth P2]Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2-
P [auth N]Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit KCP2
N [auth L2]Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit TMEM258
M [auth K2]Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4-
L [auth J]Oligosaccharyltransferase complex subunit OSTC
J [auth G]Stress-associated endoplasmic reticulum protein 1-
A [auth 5]Translocon-associated protein subunit alpha-

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
B [auth 6]IPR008856Translocon-associated protein subunit betaFamily
D [auth 8]IPR008855Translocon-associatedFamily
G [auth D]IPR002208SecY/SEC61-alpha familyFamily
G [auth D]IPR030659SecY conserved siteConserved Site
G [auth D]IPR023201SecY domain superfamilyHomologous Superfamily
G [auth D]IPR019561Translocon Sec61/SecY, plug domainDomain
K [auth I]IPR054479AglB-like, core domainDomain
K [auth I]IPR003674Oligosaccharyl transferase, STT3 subunitFamily
K [auth I]IPR048307Oligosaccharyl transferase STT3, N-terminal domainDomain
O [auth M2]IPR003038DAD/Ost2Family
Q [auth N2]IPR055459OST48, middle domainDomain
Q [auth N2]IPR005013Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48kDa subunitFamily
Q [auth N2]IPR055457OST48, N-terminal domainDomain
R [auth O2]IPR007676Ribophorin IFamily
T [auth y3]IPR003594Histidine kinase/HSP90-like ATPase domainDomain
T [auth y3]IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
T [auth y3]IPR001404Heat shock protein Hsp90 familyFamily
T [auth y3]IPR019805Heat shock protein Hsp90, conserved siteConserved Site
T [auth y3]IPR020575Heat shock protein Hsp90, N-terminalDomain
T [auth y3]IPR036890Histidine kinase/HSP90-like ATPase superfamilyHomologous Superfamily
T [auth y3]IPR037196HSP90, C-terminal domainHomologous Superfamily
I [auth F]IPR008158Protein translocase SEC61 complex, gamma subunitFamily
I [auth F]IPR001901Protein translocase complex, SecE/Sec61-gamma subunitFamily
I [auth F]IPR023391Protein translocase SecE domain superfamilyHomologous Superfamily
H [auth E]IPR030671Protein transport Sec61-beta/SbhFamily
H [auth E]IPR016482Protein transport protein SecG/Sec61-beta/SbhFamily
F [auth B]IPR026321Coiled-coil domain-containing protein 134Family
E [auth A]IPR046357Peptidyl-prolyl cis-trans isomerase domain superfamilyHomologous Superfamily
E [auth A]IPR001179FKBP-type peptidyl-prolyl cis-trans isomerase domainDomain
E [auth A]IPR044609Peptidyl-prolyl cis-trans isomerase FKBP2/11Family
C [auth 7]IPR009779Translocon-associated protein subunit gammaFamily
S [auth P2]IPR055375Ribophorin II, second domainDomain
S [auth P2]IPR055373Ribophorin II, N-terminal domainDomain
S [auth P2]IPR056790Ribophorin II, C-terminal domainDomain
S [auth P2]IPR008814Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit Swp1Family
S [auth P2]IPR055374Ribophorin II, third domainDomain
P [auth N]IPR018614Keratinocyte-associated protein 2Family
N [auth L2]IPR007915Oligosaccharyltransferase complex subunitFamily
M [auth K2]IPR051307Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4Family
M [auth K2]IPR018943OligosaccaryltransferaseFamily
M [auth K2]IPR036330Oligosaccharyltransferase subunit ost4p superfamilyHomologous Superfamily
L [auth J]IPR021149MAGT1/OST3/OST6Family
L [auth J]IPR042416Oligosaccharyltransferase complex subunit OSTCFamily
J [auth G]IPR010580Stress-associated endoplasmic reticulum proteinFamily
A [auth 5]IPR005595Translocon-associated protein (TRAP), alpha subunitFamily

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
B [auth 6]PharosP43308
D [auth 8]PharosP51571
G [auth D]PharosP61619
K [auth I]PharosP46977
O [auth M2]PharosP61803
Q [auth N2]PharosP39656
R [auth O2]PharosP04843
T [auth y3]PharosP14625
I [auth F]PharosP60059
H [auth E]PharosP60468
F [auth B]PharosQ9H6E4
E [auth A]PharosQ9NYL4
C [auth 7]PharosQ9UNL2
S [auth P2]PharosP04844
P [auth N]PharosQ8N6L1
N [auth L2]PharosP61165
M [auth K2]PharosP0C6T2
L [auth J]PharosQ9NRP0
J [auth G]PharosQ9Y6X1
A [auth 5]PharosP43307