4V4N

Structure of the Methanococcus jannaschii ribosome-SecYEBeta channel complex


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
A [auth A7]SCOP2B SuperfamilyProtein translocase subunit SecE-like8040630 3002174 SCOP2B (2022-06-29)
B [auth A8]SCOP2B SuperfamilySec-beta subunit8040632 3000289 SCOP2B (2022-06-29)
I [auth AX]SCOP2B SuperfamilySecY-like8040629 3000333 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
A [auth A7]PF00584e4v4nA71 A: extended segmentsX: Preprotein translocase SecE subunit (From Topology)H: Preprotein translocase SecE subunit (From Topology)T: Preprotein translocase SecE subunitF: PF00584ECOD (1.6)
YA [auth AG]PF01248e4v4nAG1 A: a+b three layersX: Bacillus chorismate mutase-likeH: L30e-like (From Topology)T: L30e-likeF: PF01248ECOD (1.6)
L [auth B3]PF01248e4v4nB31 A: a+b three layersX: Bacillus chorismate mutase-likeH: L30e-like (From Topology)T: L30e-likeF: PF01248ECOD (1.6)
M [auth BA]PF01015e4v4nBA1 A: beta barrelsX: Ribosomal protein L25-likeH: 40S ribosomal protein S3A N-terminal domain (From Topology)T: 40S ribosomal protein S3A N-terminal domainF: PF01015ECOD (1.6)
M [auth BA]PF01015e4v4nBA2 A: a+b two layersX: T-foldH: 40S ribosomal protein S3A C-terminal domain (From Topology)T: 40S ribosomal protein S3A C-terminal domainF: PF01015ECOD (1.6)
N [auth BB]PF00318e4v4nBB1 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Ribosomal protein S2/SIS domain (From Topology)T: Ribosomal protein S2/SIS domainF: PF00318ECOD (1.6)
O [auth BC]PF00189e4v4nBC1 A: a+b two layersX: T-foldH: Ribosomal protein S3-C (From Topology)T: Ribosomal protein S3-CF: PF00189ECOD (1.6)
O [auth BC]PF07650e4v4nBC2 A: a+b two layersX: Alpha-lytic protease prodomain-likeH: KH-domainsT: Prokaryotic type KH domain (KH-domain type II)F: PF07650ECOD (1.6)
P [auth BD]PF00163,PF01479e4v4nBD1 A: a+b two layersX: beta-GraspH: Ubiquitin-relatedT: Alpha-L RNA-binding motifF: PF00163,PF01479ECOD (1.6)
Q [auth BE]PF00900e4v4nBE2 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: PF00900ECOD (1.6)
Q [auth BE]PF00467e4v4nBE1 A: beta barrelsX: SH3H: SH3T: SH3F: PF00467ECOD (1.6)
Q [auth BE]PF01479,PF08071e4v4nBE3 A: a+b two layersX: beta-GraspH: Ubiquitin-relatedT: Alpha-L RNA-binding motifF: PF01479,PF08071ECOD (1.6)
R [auth BF]PF03719e4v4nBF3 A: a+b two layersX: Ribosomal protein S5 domain 2-like (From Topology)H: Ribosomal protein S5 domain 2-like (From Topology)T: Ribosomal protein S5 domain 2-likeF: PF03719ECOD (1.6)
R [auth BF]PF00333e4v4nBF2 A: extended segmentsX: N-terminal region in 40S ribosomal protein rpS2 (S5p) (From Topology)H: N-terminal region in 40S ribosomal protein rpS2 (S5p) (From Topology)T: N-terminal region in 40S ribosomal protein rpS2 (S5p)F: PF00333ECOD (1.6)
S [auth BG]PF01092e4v4nBG1 A: beta barrelsX: Ribosomal protein L25-likeH: Ribosomal protein L25-like (From Topology)T: Ribosomal protein L25-likeF: PF01092ECOD (1.6)
B [auth A8]PF03911e4v4nA81 A: extended segmentsX: Sec-beta subunit (From Topology)H: Sec-beta subunit (From Topology)T: Sec-beta subunitF: PF03911ECOD (1.6)
T [auth BH]PF00177e4v4nBH1 A: alpha arraysX: Ribosomal protein S7 (From Topology)H: Ribosomal protein S7 (From Topology)T: Ribosomal protein S7F: PF00177ECOD (1.6)
U [auth BI]PF00410e4v4nBI2 A: a+b two layersX: R3H domain-likeH: Ribosomal protein S8, N-terminal domain (From Topology)T: Ribosomal protein S8, N-terminal domainF: PF00410ECOD (1.6)
U [auth BI]PF00410e4v4nBI1 A: a+b two layersX: Ribosomal protein S8, C-terminal domain (From Topology)H: Ribosomal protein S8, C-terminal domain (From Topology)T: Ribosomal protein S8, C-terminal domainF: PF00410ECOD (1.6)
V [auth BJ]PF01201e4v4nBJ1 A: beta barrelsX: Ribosomal protein L14-likeH: Ribosomal protein L14-related (From Topology)T: Ribosomal protein L14-relatedF: PF01201ECOD (1.6)
W [auth BK]PF00380e4v4nBK1 A: a+b two layersX: Ribosomal protein S5 domain 2-like (From Topology)H: Ribosomal protein S5 domain 2-like (From Topology)T: Ribosomal protein S5 domain 2-likeF: PF00380ECOD (1.6)
X [auth BL]PF00338e4v4nBL1 A: a+b two layersX: Alpha-beta plaitsH: Ribosomal protein S10 (From Topology)T: Ribosomal protein S10F: PF00338ECOD (1.6)
Y [auth BM]PF00411e4v4nBM1 A: mixed a+b and a/bX: Ribonuclease H-likeH: Ribonuclease H-like (From Topology)T: Ribonuclease H-likeF: PF00411ECOD (1.6)
Z [auth BN]PF00164e4v4nBN1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: PF00164ECOD (1.6)
AA [auth BO]PF00416e4v4nBO1 A: alpha arraysX: HhH/H2THH: H2TH (From Topology)T: H2THF: PF00416ECOD (1.6)
BA [auth BP]PF00253e4v4nBP1 A: few secondary structure elementsX: Glucocorticoid receptor-likeH: LIM domain-likeT: LIM domain-likeF: PF00253ECOD (1.6)
CA [auth BQ]PF08069e4v4nBQ1 A: alpha arraysX: HTHH: 40S ribosomal protein S13 N-terminal domain (From Topology)T: 40S ribosomal protein S13 N-terminal domainF: PF08069ECOD (1.6)
CA [auth BQ]PF00312e4v4nBQ2 A: alpha arraysX: S15/NS1 RNA-binding domain (From Topology)H: S15/NS1 RNA-binding domain (From Topology)T: S15/NS1 RNA-binding domainF: PF00312ECOD (1.6)
C [auth Af]PF00832e4v4nAf1 A: extended segmentsX: Ribosomal protein L39e (From Topology)H: Ribosomal protein L39e (From Topology)T: Ribosomal protein L39eF: PF00832ECOD (1.6)
DA [auth BR]PF00366e4v4nBR1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: PF00366ECOD (1.6)
EA [auth BS]PF00833e4v4nBS1 A: alpha arraysX: HTHH: HTHT: FF domainF: PF00833ECOD (1.6)
FA [auth BT]PF00203e4v4nBT1 A: a+b two layersX: Ribosomal protein S19 (From Topology)H: Ribosomal protein S19 (From Topology)T: Ribosomal protein S19F: PF00203ECOD (1.6)
GA [auth BU]PF01090e4v4nBU1 A: alpha arraysX: HTHH: HTHT: wingedF: PF01090ECOD (1.6)
HA [auth BV]PF01282e4v4nBV1 A: a+b two layersX: Alpha-beta plaitsH: Ribosomal proteins S24e, L23 and L15e (From Topology)T: Ribosomal proteins S24e, L23 and L15eF: PF01282ECOD (1.6)
IA [auth BW]PF01667e4v4nBW1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: PF01667ECOD (1.6)
JA [auth BX]PF01200e4v4nBX1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: PF01200ECOD (1.6)
KA [auth BY]PF01599e4v4nBY1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: PF01599ECOD (1.6)
D [auth AQ]PF01280e4v4nAQ1 A: alpha arraysX: Ribosomal protein L19 (L19e) N-terminal domain (From Topology)H: Ribosomal protein L19 (L19e) N-terminal domain (From Topology)T: Ribosomal protein L19 (L19e) N-terminal domainF: PF01280ECOD (1.6)
D [auth AQ]PF01280e4v4nAQ2 A: alpha bundlesX: Ribosomal protein L19 (L19e) C-terminal domain (From Topology)H: Ribosomal protein L19 (L19e) C-terminal domain (From Topology)T: Ribosomal protein L19 (L19e) C-terminal domainF: PF01280ECOD (1.6)
GB [auth AK]PF00467e4v4nAK1 A: beta barrelsX: SH3H: SH3T: SH3F: PF00467ECOD (1.6)
NA [auth A5]PF00467e4v4nA51 A: beta barrelsX: SH3H: SH3T: SH3F: PF00467ECOD (1.6)
OA [auth AA]PF00687e4v4nAA2 A: a+b two layersX: a+b domain in Ribosomal protein L1 (From Topology)H: a+b domain in Ribosomal protein L1 (From Topology)T: a+b domain in Ribosomal protein L1F: PF00687ECOD (1.6)
OA [auth AA]PF00687e4v4nAA1 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Rossmann-like domain in Ribosomal protein L1 (From Topology)T: Rossmann-like domain in Ribosomal protein L1F: PF00687ECOD (1.6)
PA [auth Aa]PF01198e4v4nAa1 A: a+b two layersX: Ribosomal protein L31e-likeH: Ribosomal protein L31e/gp120 outer domain (From Topology)T: Ribosomal protein L31e/gp120 outer domainF: PF01198ECOD (1.6)
QA [auth AB]PF00181e4v4nAB2 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: PF00181ECOD (1.6)
QA [auth AB]PF03947e4v4nAB1 A: beta barrelsX: SH3H: SH3T: SH3F: PF03947ECOD (1.6)
RA [auth Ab]PF01655e4v4nAb1 A: a/b three-layered sandwichesX: Ribosomal protein L13/L15p/L18e/L32eH: Ribosomal protein L32e (From Topology)T: Ribosomal protein L32eF: PF01655ECOD (1.6)
SA [auth AC]PF00297e4v4nAC1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Alanine racemase-CF: PF00297ECOD (1.6)
TA [auth AD]PF00573e4v4nAD1 A: a/b three-layered sandwichesX: Ribosomal protein L4 (From Topology)H: Ribosomal protein L4 (From Topology)T: Ribosomal protein L4F: PF00573ECOD (1.6)
UA [auth Ad]PF01199e4v4nAd1 A: few secondary structure elementsX: Glucocorticoid receptor-likeH: RPL34 (From Topology)T: RPL34F: PF01199ECOD (1.6)
VA [auth AE]PF00281,PF00673e4v4nAE1 A: a+b two layersX: Ribosomal protein L5 (From Topology)H: Ribosomal protein L5 (From Topology)T: Ribosomal protein L5F: PF00281,PF00673ECOD (1.6)
WA [auth Ae]PF01907e4v4nAe1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: PF01907ECOD (1.6)
E [auth AS]PF00237e4v4nAS1 A: a+b two layersX: Enolase-N/ribosomal proteinH: Ribosomal protein L22 (From Topology)T: Ribosomal protein L22F: PF00237ECOD (1.6)
XA [auth AF]PF00347e4v4nAF2 A: a+b two layersX: Ribosomal protein L6 (From Topology)H: Ribosomal protein L6 (From Topology)T: Ribosomal protein L6F: PF00347ECOD (1.6)
ZA [auth Ag]F_UNCLASSIFIEDe4v4nAg1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: F_UNCLASSIFIEDECOD (1.6)
AB [auth AH]PF00298e4v4nAH2 A: alpha arraysX: HTHH: HTHT: Ribosomal protein L11, C-terminal domainF: PF00298ECOD (1.6)
AB [auth AH]PF03946e4v4nAH1 A: a+b two layersX: Ribosomal protein L11/L12e N-terminal domain-likeH: Ribosomal protein L11/L12e N-terminal domain (From Topology)T: Ribosomal protein L11/L12e N-terminal domainF: PF03946ECOD (1.6)
BB [auth Ah]F_UNCLASSIFIEDe4v4nAh1 A: extended segmentsX: Ribosomal protein L41-A (From Topology)H: Ribosomal protein L41-A (From Topology)T: Ribosomal protein L41-AF: F_UNCLASSIFIEDECOD (1.6)
CB [auth AI]PF00572e4v4nAI1 A: a/b three-layered sandwichesX: Ribosomal protein L13/L15p/L18e/L32eH: Ribosomal protein L13 and L16-A (From Topology)T: Ribosomal protein L13 and L16-AF: PF00572ECOD (1.6)
DB [auth Ai]PF01780e4v4nAi1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: PF01780ECOD (1.6)
EB [auth AJ]PF00238e4v4nAJ1 A: beta barrelsX: Ribosomal protein L14-likeH: Ribosomal protein L14-related (From Topology)T: Ribosomal protein L14-relatedF: PF00238ECOD (1.6)
FB [auth Aj]PF00935e4v4nAj1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: PF00935ECOD (1.6)
HB [auth Ak]PF00466e4v4nAk2 A: a+b two layersX: Alpha-beta plaitsH: Ribosomal protein L10-like (From Topology)T: Ribosomal protein L10-likeF: PF00466ECOD (1.6)
HB [auth Ak]PF17777e4v4nAk1 A: a+b two layersX: Insertion domain in 60S ribosomal protein rpP0 (L10P) (From Topology)H: Insertion domain in 60S ribosomal protein rpP0 (L10P) (From Topology)T: Insertion domain in 60S ribosomal protein rpP0 (L10P)F: PF17777ECOD (1.6)
IB [auth AL]PF00828e4v4nAL1 A: a/b three-layered sandwichesX: Ribosomal protein L13/L15p/L18e/L32eH: Ribosomal proteins L15p and L18e (From Topology)T: Ribosomal proteins L15p and L18eF: PF00828ECOD (1.6)
F [auth AT]PF00276e4v4nAT1 A: a+b two layersX: Alpha-beta plaitsH: Ribosomal proteins S24e, L23 and L15e (From Topology)T: Ribosomal proteins S24e, L23 and L15eF: PF00276ECOD (1.6)
JB [auth AM]PF00827e4v4nAM1 A: a+b two layersX: Alpha-beta plaitsH: Ribosomal proteins S24e, L23 and L15e (From Topology)T: Ribosomal proteins S24e, L23 and L15eF: PF00827ECOD (1.6)
KB [auth AN]PF00252e4v4nAN1 A: a+b complex topologyX: alpha/beta-Hammerhead/Barrel-sandwich hybridH: alpha/beta-Hammerhead/Barrel-sandwich hybridT: Ribosomal protein L10eF: PF00252ECOD (1.6)
LB [auth AO]PF17144e4v4nAO1 A: mixed a+b and a/bX: Ribonuclease H-likeH: Ribonuclease H-like (From Topology)T: Ribonuclease H-likeF: PF17144ECOD (1.6)
MB [auth AP]PF17135e4v4nAP1 A: a/b three-layered sandwichesX: Ribosomal protein L13/L15p/L18e/L32eH: Ribosomal proteins L15p and L18e (From Topology)T: Ribosomal proteins L15p and L18eF: PF17135ECOD (1.6)
NB [auth AR]PF01157e4v4nAR1 A: beta barrelsX: SH3H: SH3T: SH3F: PF01157ECOD (1.6)
OB [auth AV]PF01246e4v4nAV1 A: few secondary structure elementsX: Glucocorticoid receptor-likeH: LIM domain-likeT: LIM domain-likeF: PF01246ECOD (1.6)
PB [auth AY]PF00327e4v4nAY1 A: a+b two layersX: Ribosomal protein L30p/L7e (From Topology)H: Ribosomal protein L30p/L7e (From Topology)T: Ribosomal protein L30p/L7eF: PF00327ECOD (1.6)
QB [auth AZ]PF01248e4v4nAZ1 A: a+b three layersX: Bacillus chorismate mutase-likeH: L30e-like (From Topology)T: L30e-likeF: PF01248ECOD (1.6)
G [auth AU]PF16906e4v4nAU1 A: beta barrelsX: SH3H: SH3T: SH3F: PF16906ECOD (1.6)
H [auth AW]PF00831e4v4nAW1 A: alpha bundlesX: Long alpha-hairpinH: Ribosomal protein L29 (L29p) (From Topology)T: Ribosomal protein L29 (L29p)F: PF00831ECOD (1.6)
I [auth AX]PF00344,PF10559e4v4nAX1 A: alpha complex topologyX: Preprotein translocase SecY subunit (From Topology)H: Preprotein translocase SecY subunit (From Topology)T: Preprotein translocase SecY subunitF: PF00344,PF10559ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A [auth A7]PF00584SecE/Sec61-gamma subunits of protein translocation complex (SecE)SecE/Sec61-gamma subunits of protein translocation complex- Family
B [auth A8]PF03911Sec61beta family (Sec61_beta)Sec61beta family- Family
I [auth AX]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
I [auth AX]PF00344SecY (SecY)SecY- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth A7]Preprotein translocase subunit SecE
J [auth B1]E-tRNA---
K [auth B2]16S ribosomal RNA---
L [auth B3],
YA [auth AG]
30S ribosomal protein L7AE---
M [auth BA]30S ribosomal protein S3AE---
N [auth BB]30S ribosomal protein S2P---
O [auth BC]30S ribosomal protein S3P---
P [auth BD]30S ribosomal protein S4P---
Q [auth BE]30S ribosomal protein S4E---
R [auth BF]30S ribosomal protein S5P---
S [auth BG]30S ribosomal protein S6E---
B [auth A8]Preprotein translocase subunit SecG-
T [auth BH]30S ribosomal protein S7P---
U [auth BI]30S ribosomal protein S8P---
V [auth BJ]30S ribosomal protein S8E---
W [auth BK]30S ribosomal protein S9P---
X [auth BL]30S ribosomal protein S10P---
Y [auth BM]30S ribosomal protein S11P---
Z [auth BN]30S ribosomal protein S12P---
AA [auth BO]30S ribosomal protein S13P---
BA [auth BP]30S ribosomal protein S14P---
CA [auth BQ]30S ribosomal protein S15P/S13E---
C [auth Af]50S ribosomal protein L39E---
DA [auth BR]30S ribosomal protein S17P---
EA [auth BS]30S ribosomal protein S17E---
FA [auth BT]30S ribosomal protein S19P---
GA [auth BU]30S ribosomal protein S19E---
HA [auth BV]30S ribosomal protein S24E---
IA [auth BW]30S ribosomal protein S27E---
JA [auth BX]30S ribosomal protein S28E---
KA [auth BY]30S ribosomal protein S27AE---
LA [auth A1]23S ribosomal RNA---
MA [auth A3]5S ribosomal RNA---
D [auth AQ]50S ribosomal protein L19E---
GB [auth AK],
NA [auth A5]
50S ribosomal protein L14E---
OA [auth AA]50S ribosomal protein L1P---
PA [auth Aa]50S ribosomal protein L31E---
QA [auth AB]50S ribosomal protein L2---
RA [auth Ab]50S ribosomal protein L32E---
SA [auth AC]50S ribosomal protein L3P---
TA [auth AD]50S ribosomal protein L4P---
UA [auth Ad]50S ribosomal protein L34E---
VA [auth AE]50S ribosomal protein L5P---
WA [auth Ae]50S ribosomal protein L37E---
E [auth AS]50S ribosomal protein L22P---
XA [auth AF]50S ribosomal protein L6P---
ZA [auth Ag]50S ribosomal protein L40E---
AB [auth AH]50S ribosomal protein L11P---
BB [auth Ah]50S ribosomal protein L41E---
CB [auth AI]50S ribosomal protein L13P---
DB [auth Ai]50S ribosomal protein L37AE---
EB [auth AJ]50S ribosomal protein L14P---
FB [auth Aj]50S ribosomal protein L44E---
HB [auth Ak]50S ribosomal protein P0/L10E---
IB [auth AL]50S ribosomal protein L15P---
F [auth AT]50S ribosomal protein L23P---
JB [auth AM]50S ribosomal protein L15E---
KB [auth AN]50S ribosomal protein L10E/L16---
LB [auth AO]50S ribosomal protein L18P---
MB [auth AP]50S ribosomal protein L18E---
NB [auth AR]50S ribosomal protein L21E---
OB [auth AV]50S ribosomal protein L24E---
PB [auth AY]50S ribosomal protein L30P---
QB [auth AZ]50S ribosomal protein L30E---
G [auth AU]50S ribosomal protein L24P---
H [auth AW]50S ribosomal protein L29P---
I [auth AX]Protein translocase subunit SecY