2wwb

CRYO-EM STRUCTURE OF THE MAMMALIAN SEC61 COMPLEX BOUND TO THE ACTIVELY TRANSLATING WHEAT GERM 80S RIBOSOME

Method: ELECTRON MICROSCOPY D_max: 154.9 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 1

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Heteromer Protein × 11 RNA 4 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain A； UniProt 1–476	Not recorded	PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT GAMMA × 1 （P60058） PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT BETA × 1 （P60467） 5.8S RRNA × 1 25S RRNA × 1 25S RRNA × 1 25S RRNA × 1 60S RIBOSOMAL PROTEIN L4-B × 1 60S RIBOSOMAL PROTEIN L17-A × 1 60S RIBOSOMAL PROTEIN L19 × 1 60S RIBOSOMAL PROTEIN L25 × 1 60S RIBOSOMAL PROTEIN L26-A × 1 60S RIBOSOMAL PROTEIN L31-A × 1 60S RIBOSOMAL PROTEIN L35 × 1 60S RIBOSOMAL PROTEIN L39 × 1	ELECTRON MICROSCOPY cryo-EM buffer：30 MM HEPES/KOH, PH 7.5 180 MM KOAC, 10 MM MG(OAC)2, 1 MM DTT, 3.5 % (W/V) GLYCEROL 0.3 % (W/V) DIGITONIN；pH 7.5；30 MM HEPES/KOH, PH 7.5 180 MM KOAC, 10 MM MG(OAC)2, 1 MM DTT, 3.5 % (W/V) GLYCEROL 0.3 % (W/V) DIGITONIN cryo-EM vitrification conditions：Cryogen ETHANE；CRYOGEN- ETHANE, HUMIDITY- 95, INSTRUMENT- VITROBOT, METHOD- BLOT FOR 10 SECONDS BEFORE PLUNGING, USE 2 LAYERS OF FILTER PAPER	Resolution 6.48 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 2WWB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3JC2 The structure of the mammalian Sec61 channel opened by a signal sequence Deposited 2015-11-15	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain 1 1–476（476 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50 mM HEPES, 200 mM potassium acetate, 15 mM magnesium acetate, 1 mM DTT, 0.25% Digitonin；pH 7.5；50 mM HEPES, 200 mM potassium acetate, 15 mM magnesium acetate, 1 mM DTT, 0.25% Digitonin cryo-EM vitrification conditions 3 uL sample was added to the grid, incubated for 30 seconds at 4 C, blotted for 9 seconds；Cryogen ETHANE；3 uL sample was added to the grid, incubated for 30 seconds at 4 C, blotted for 9 seconds, and then plunged into liquid ethane (FEI VITROBOT).	Resolution 3.60 Å
4CG5 Cryo-EM of the Sec61-complex bound to the 80S ribosome translating a secretory substrate Deposited 2013-11-21	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–476（476 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 30 MM HEPES/KOH 7.6, 10 MM MG(OAC)2, 180 MM KOAC/HAC PH 7.6, 0.3 % DIGITONIN, 1 MM DTT；pH 7.6；30 MM HEPES/KOH 7.6, 10 MM MG(OAC)2, 180 MM KOAC/HAC PH 7.6, 0.3 % DIGITONIN, 1 MM DTT cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 95, INSTRUMENT- FEI VITROBOT MARK IV, METHOD- BLOT FOR 3 SECONDS BEFORE PLUNGING,	Resolution 7.40 Å
4CG6 Cryo-em of the Sec61-complex bound to the 80s ribosome translating a membrane-inserting substrate Deposited 2013-11-21	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–476（476 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 30 MM HEPES/KOH 7.6, 10 MM MG(OAC)2, 180 MM KOAC/HAC PH 7.6, 0.3 % DIGITONIN, 1 MM DTT；pH 7.6；30 MM HEPES/KOH 7.6, 10 MM MG(OAC)2, 180 MM KOAC/HAC PH 7.6, 0.3 % DIGITONIN, 1 MM DTT cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 95, INSTRUMENT- FEI VITROBOT MARK IV, METHOD- BLOT FOR 3 SECONDS BEFORE PLUNGING,	Resolution 7.80 Å
4CG7 Cryo-EM of the Sec61-complex bound to the idle 80S ribosome Deposited 2013-11-21	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–476（476 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 30 MM HEPES/KOH 7.6, 10 MM MG(OAC)2, 180 MM KOAC/HAC PH 7.6, 0.3 % DIGITONIN, 1 MM DTT；pH 7.6；30 MM HEPES/KOH 7.6, 10 MM MG(OAC)2, 180 MM KOAC/HAC PH 7.6, 0.3 % DIGITONIN, 1 MM DTT cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 95, INSTRUMENT- FEI VITROBOT MARK IV, METHOD- BLOT FOR 3 SECONDS BEFORE PLUNGING,	Resolution 6.90 Å
5A6U Native mammalian ribosome-bound Sec61 protein-conducting channel in the 'non-inserting' state Deposited 2015-07-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 26–476（451 aa） Fragment：UNP RESIDUES 26-476	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 20MM HEPES, 50MM KCL, 2MM MGCL2；pH 7.6；20MM HEPES, 50MM KCL, 2MM MGCL2 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；VITRIFICATION 1 -- CRYOGEN- ETHANE-PROPANE MIXTURE, HUMIDITY- 70, INSTRUMENT- FEI VITROBOT MARK IV, METHOD- BLOT 3 SECONDS BEFORE PLUNGING.,	Resolution 9.00 Å
6FTG Subtomogram average of OST-containing ribosome-translocon complexes from canine rough microsomal membranes Deposited 2018-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric	Chain x 5–465（461 aa）	Not recorded	MG MAGNESIUM ION × 159 ZN ZINC ION × 5 9UB [(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]methyl-[oxidanyl-[(2~{Z},6~{Z},10~{Z})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenoxy]phosphoryl]oxy-phosphinic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Blot 3 seconds before plunging.	Resolution 9.10 Å
6FTI Cryo-EM Structure of the Mammalian Oligosaccharyltransferase Bound to Sec61 and the Programmed 80S Ribosome Deposited 2018-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric	Chain x 5–465（461 aa）	Not recorded	MG MAGNESIUM ION × 159 ZN ZINC ION × 5 9UB [(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]methyl-[oxidanyl-[(2~{Z},6~{Z},10~{Z})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenoxy]phosphoryl]oxy-phosphinic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
6FTJ Cryo-EM Structure of the Mammalian Oligosaccharyltransferase Bound to Sec61 and the Non-programmed 80S Ribosome Deposited 2018-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric	Chain x 5–465（461 aa）	Not recorded	MG MAGNESIUM ION × 159 ZN ZINC ION × 5 9UB [(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]methyl-[oxidanyl-[(2~{Z},6~{Z},10~{Z})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenoxy]phosphoryl]oxy-phosphinic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.70 Å
6R7Q Structure of XBP1u-paused ribosome nascent chain complex with Sec61. Deposited 2019-03-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 88-meric	Chain XX 5–465（461 aa）	Not recorded	ZN ZINC ION × 6 MG MAGNESIUM ION × 299	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
6Z3T Structure of canine Sec61 inhibited by mycolactone Deposited 2020-05-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–476（476 aa）	Not recorded	Q6B [(6~{S},7~{S},9~{Z},12~{R})-12-[(~{Z},2~{S},6~{R},7~{R},9~{R})-4,6-dimethyl-7,9-bis(oxidanyl)dec-4-en-2-yl]-7,9-dimethyl-2-oxidanylidene-1-oxacyclododec-9-en-6-yl] (2~{E},4~{E},6~{E},8~{E},10~{E},12~{S},13~{S},15~{S})-4,6,10-trimethyl-12,13,15-tris(oxidanyl)hexadeca-2,4,6,8,10-pentaenoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Blot time 5 seconds Blot force -15 Incubation time 15 seconds	Resolution 2.69 Å
7TM3 Structure of the rabbit 80S ribosome stalled on a 2-TMD Rhodopsin intermediate in complex with the multipass translocon Deposited 2022-01-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 54-meric	Chain 1 1–476（476 aa）	Not recorded	MG MAGNESIUM ION × 220 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50 mM HEPES-KOH, pH 7.5, 200 mM KOAc, 5 mM Mg(OAc)2, 0.25% digitonin, 50 mM biotin cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 sec with Whatman filter papers at a blot force of -15 before plunging	Resolution 3.25 Å
7TUT Structure of the rabbit 80S ribosome stalled on a 4-TMD Rhodopsin intermediate in complex with the multipass translocon Deposited 2022-02-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric	Chain 1 1–476（476 aa）	Not recorded	MG MAGNESIUM ION × 220 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50 mM HEPES-KOH, pH 7.5, 200 mM potassium acetate, 5 mM magnesium acetate, 0.25% digitonin, 50 mM biotin cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds with Whatman filter papers at a blot force of -15 before plunging.	Resolution 3.88 Å
8BTK Structure of the TRAP complex with the Sec translocon and a translating ribosome Deposited 2022-11-29	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 86 PDB declaration: 92-meric	Chain SX 1–476（476 aa）	Not recorded	SPD SPERMIDINE × 30 SPM SPERMINE × 3 MG MAGNESIUM ION × 750 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 AAC ACETYLAMINO-ACETIC ACID × 1 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；3.5 uL of sample was incubated on the grid for 60 seconds at 4*C and 100% humidity before being blotted and plunged into liquid ethane/propane mix cooled to liquid nitrogen temperature	Resolution 3.50 Å
8OJ0 60S ribosomal subunit bound to the E3-UFM1 complex - state 2 (native) Deposited 2023-03-23	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric	Chain 1 1–476（476 aa）	Not recorded	MG MAGNESIUM ION × 220 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8OJ8 60S ribosomal subunit bound to the E3-UFM1 complex - state 1 (native) Deposited 2023-03-24	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric	Chain 1 1–476（476 aa）	Not recorded	MG MAGNESIUM ION × 220 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8RJB Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-RAMP4 Deposited 2023-12-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 51-meric	Chain 1 1–476（476 aa）	Not recorded	MG MAGNESIUM ION × 218 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.69 Å
8RJC Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 1 Deposited 2023-12-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric	Chain 1 1–476（476 aa）	Not recorded	MG MAGNESIUM ION × 218 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8RJD Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 2 Deposited 2023-12-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric	Chain 1 1–476（476 aa）	Not recorded	MG MAGNESIUM ION × 218 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.79 Å

18 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	S61A1_CANFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–476； UniProt 1–476

PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT GAMMA

OrganismNot specified

UniProt P60058

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Heteromer Protein × 11 RNA 4 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain B； UniProt 1–68	Not recorded	PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 1 × 1 （P38377） PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT BETA × 1 （P60467） 5.8S RRNA × 1 25S RRNA × 1 25S RRNA × 1 25S RRNA × 1 60S RIBOSOMAL PROTEIN L4-B × 1 60S RIBOSOMAL PROTEIN L17-A × 1 60S RIBOSOMAL PROTEIN L19 × 1 60S RIBOSOMAL PROTEIN L25 × 1 60S RIBOSOMAL PROTEIN L26-A × 1 60S RIBOSOMAL PROTEIN L31-A × 1 60S RIBOSOMAL PROTEIN L35 × 1 60S RIBOSOMAL PROTEIN L39 × 1	ELECTRON MICROSCOPY cryo-EM buffer：30 MM HEPES/KOH, PH 7.5 180 MM KOAC, 10 MM MG(OAC)2, 1 MM DTT, 3.5 % (W/V) GLYCEROL 0.3 % (W/V) DIGITONIN；pH 7.5；30 MM HEPES/KOH, PH 7.5 180 MM KOAC, 10 MM MG(OAC)2, 1 MM DTT, 3.5 % (W/V) GLYCEROL 0.3 % (W/V) DIGITONIN cryo-EM vitrification conditions：Cryogen ETHANE；CRYOGEN- ETHANE, HUMIDITY- 95, INSTRUMENT- VITROBOT, METHOD- BLOT FOR 10 SECONDS BEFORE PLUNGING, USE 2 LAYERS OF FILTER PAPER	Resolution 6.48 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 2WWB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3JC2 The structure of the mammalian Sec61 channel opened by a signal sequence Deposited 2015-11-15	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain 2 7–68（62 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50 mM HEPES, 200 mM potassium acetate, 15 mM magnesium acetate, 1 mM DTT, 0.25% Digitonin；pH 7.5；50 mM HEPES, 200 mM potassium acetate, 15 mM magnesium acetate, 1 mM DTT, 0.25% Digitonin cryo-EM vitrification conditions 3 uL sample was added to the grid, incubated for 30 seconds at 4 C, blotted for 9 seconds；Cryogen ETHANE；3 uL sample was added to the grid, incubated for 30 seconds at 4 C, blotted for 9 seconds, and then plunged into liquid ethane (FEI VITROBOT).	Resolution 3.60 Å
4CG5 Cryo-EM of the Sec61-complex bound to the 80S ribosome translating a secretory substrate Deposited 2013-11-21	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–68（68 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 30 MM HEPES/KOH 7.6, 10 MM MG(OAC)2, 180 MM KOAC/HAC PH 7.6, 0.3 % DIGITONIN, 1 MM DTT；pH 7.6；30 MM HEPES/KOH 7.6, 10 MM MG(OAC)2, 180 MM KOAC/HAC PH 7.6, 0.3 % DIGITONIN, 1 MM DTT cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 95, INSTRUMENT- FEI VITROBOT MARK IV, METHOD- BLOT FOR 3 SECONDS BEFORE PLUNGING,	Resolution 7.40 Å
4CG6 Cryo-em of the Sec61-complex bound to the 80s ribosome translating a membrane-inserting substrate Deposited 2013-11-21	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–68（68 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 30 MM HEPES/KOH 7.6, 10 MM MG(OAC)2, 180 MM KOAC/HAC PH 7.6, 0.3 % DIGITONIN, 1 MM DTT；pH 7.6；30 MM HEPES/KOH 7.6, 10 MM MG(OAC)2, 180 MM KOAC/HAC PH 7.6, 0.3 % DIGITONIN, 1 MM DTT cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 95, INSTRUMENT- FEI VITROBOT MARK IV, METHOD- BLOT FOR 3 SECONDS BEFORE PLUNGING,	Resolution 7.80 Å
4CG7 Cryo-EM of the Sec61-complex bound to the idle 80S ribosome Deposited 2013-11-21	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–68（68 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 30 MM HEPES/KOH 7.6, 10 MM MG(OAC)2, 180 MM KOAC/HAC PH 7.6, 0.3 % DIGITONIN, 1 MM DTT；pH 7.6；30 MM HEPES/KOH 7.6, 10 MM MG(OAC)2, 180 MM KOAC/HAC PH 7.6, 0.3 % DIGITONIN, 1 MM DTT cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 95, INSTRUMENT- FEI VITROBOT MARK IV, METHOD- BLOT FOR 3 SECONDS BEFORE PLUNGING,	Resolution 6.90 Å
5A6U Native mammalian ribosome-bound Sec61 protein-conducting channel in the 'non-inserting' state Deposited 2015-07-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 7–68（62 aa） Fragment：UNP RESIDUES 7-68	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 20MM HEPES, 50MM KCL, 2MM MGCL2；pH 7.6；20MM HEPES, 50MM KCL, 2MM MGCL2 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；VITRIFICATION 1 -- CRYOGEN- ETHANE-PROPANE MIXTURE, HUMIDITY- 70, INSTRUMENT- FEI VITROBOT MARK IV, METHOD- BLOT 3 SECONDS BEFORE PLUNGING.,	Resolution 9.00 Å
6FTG Subtomogram average of OST-containing ribosome-translocon complexes from canine rough microsomal membranes Deposited 2018-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric	Chain y 7–68（62 aa）	Not recorded	MG MAGNESIUM ION × 159 ZN ZINC ION × 5 9UB [(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]methyl-[oxidanyl-[(2~{Z},6~{Z},10~{Z})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenoxy]phosphoryl]oxy-phosphinic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Blot 3 seconds before plunging.	Resolution 9.10 Å
6FTI Cryo-EM Structure of the Mammalian Oligosaccharyltransferase Bound to Sec61 and the Programmed 80S Ribosome Deposited 2018-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric	Chain y 7–68（62 aa）	Not recorded	MG MAGNESIUM ION × 159 ZN ZINC ION × 5 9UB [(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]methyl-[oxidanyl-[(2~{Z},6~{Z},10~{Z})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenoxy]phosphoryl]oxy-phosphinic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
6FTJ Cryo-EM Structure of the Mammalian Oligosaccharyltransferase Bound to Sec61 and the Non-programmed 80S Ribosome Deposited 2018-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric	Chain y 7–68（62 aa）	Not recorded	MG MAGNESIUM ION × 159 ZN ZINC ION × 5 9UB [(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]methyl-[oxidanyl-[(2~{Z},6~{Z},10~{Z})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenoxy]phosphoryl]oxy-phosphinic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.70 Å
6R7Q Structure of XBP1u-paused ribosome nascent chain complex with Sec61. Deposited 2019-03-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 88-meric	Chain YY 7–68（62 aa）	Not recorded	ZN ZINC ION × 6 MG MAGNESIUM ION × 299	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
6Z3T Structure of canine Sec61 inhibited by mycolactone Deposited 2020-05-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–68（68 aa）	Not recorded	Q6B [(6~{S},7~{S},9~{Z},12~{R})-12-[(~{Z},2~{S},6~{R},7~{R},9~{R})-4,6-dimethyl-7,9-bis(oxidanyl)dec-4-en-2-yl]-7,9-dimethyl-2-oxidanylidene-1-oxacyclododec-9-en-6-yl] (2~{E},4~{E},6~{E},8~{E},10~{E},12~{S},13~{S},15~{S})-4,6,10-trimethyl-12,13,15-tris(oxidanyl)hexadeca-2,4,6,8,10-pentaenoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Blot time 5 seconds Blot force -15 Incubation time 15 seconds	Resolution 2.69 Å
8BTK Structure of the TRAP complex with the Sec translocon and a translating ribosome Deposited 2022-11-29	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 86 PDB declaration: 92-meric	Chain SY 1–68（68 aa）	Not recorded	SPD SPERMIDINE × 30 SPM SPERMINE × 3 MG MAGNESIUM ION × 750 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 AAC ACETYLAMINO-ACETIC ACID × 1 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；3.5 uL of sample was incubated on the grid for 60 seconds at 4*C and 100% humidity before being blotted and plunged into liquid ethane/propane mix cooled to liquid nitrogen temperature	Resolution 3.50 Å
8RJB Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-RAMP4 Deposited 2023-12-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 51-meric	Chain 3 1–68（68 aa）	Not recorded	MG MAGNESIUM ION × 218 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.69 Å
8RJC Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 1 Deposited 2023-12-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric	Chain 3 1–68（68 aa）	Not recorded	MG MAGNESIUM ION × 218 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8RJD Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 2 Deposited 2023-12-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric	Chain 3 1–68（68 aa）	Not recorded	MG MAGNESIUM ION × 218 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.79 Å

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SC61G_CANFA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–68； UniProt 1–68

PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT BETA

OrganismNot specified

UniProt P60467

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Heteromer Protein × 11 RNA 4 PDB declaration: pentadecameric（15） Consistent with all polymer counts	Chain C； UniProt 1–96	Not recorded	PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 1 × 1 （P38377） PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT GAMMA × 1 （P60058） 5.8S RRNA × 1 25S RRNA × 1 25S RRNA × 1 25S RRNA × 1 60S RIBOSOMAL PROTEIN L4-B × 1 60S RIBOSOMAL PROTEIN L17-A × 1 60S RIBOSOMAL PROTEIN L19 × 1 60S RIBOSOMAL PROTEIN L25 × 1 60S RIBOSOMAL PROTEIN L26-A × 1 60S RIBOSOMAL PROTEIN L31-A × 1 60S RIBOSOMAL PROTEIN L35 × 1 60S RIBOSOMAL PROTEIN L39 × 1	ELECTRON MICROSCOPY cryo-EM buffer：30 MM HEPES/KOH, PH 7.5 180 MM KOAC, 10 MM MG(OAC)2, 1 MM DTT, 3.5 % (W/V) GLYCEROL 0.3 % (W/V) DIGITONIN；pH 7.5；30 MM HEPES/KOH, PH 7.5 180 MM KOAC, 10 MM MG(OAC)2, 1 MM DTT, 3.5 % (W/V) GLYCEROL 0.3 % (W/V) DIGITONIN cryo-EM vitrification conditions：Cryogen ETHANE；CRYOGEN- ETHANE, HUMIDITY- 95, INSTRUMENT- VITROBOT, METHOD- BLOT FOR 10 SECONDS BEFORE PLUNGING, USE 2 LAYERS OF FILTER PAPER	Resolution 6.48 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 2WWB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4CG5 Cryo-EM of the Sec61-complex bound to the 80S ribosome translating a secretory substrate Deposited 2013-11-21	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 61–96（36 aa） Fragment：RESIDUES 61-96	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 30 MM HEPES/KOH 7.6, 10 MM MG(OAC)2, 180 MM KOAC/HAC PH 7.6, 0.3 % DIGITONIN, 1 MM DTT；pH 7.6；30 MM HEPES/KOH 7.6, 10 MM MG(OAC)2, 180 MM KOAC/HAC PH 7.6, 0.3 % DIGITONIN, 1 MM DTT cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 95, INSTRUMENT- FEI VITROBOT MARK IV, METHOD- BLOT FOR 3 SECONDS BEFORE PLUNGING,	Resolution 7.40 Å
4CG6 Cryo-em of the Sec61-complex bound to the 80s ribosome translating a membrane-inserting substrate Deposited 2013-11-21	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–96（96 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 30 MM HEPES/KOH 7.6, 10 MM MG(OAC)2, 180 MM KOAC/HAC PH 7.6, 0.3 % DIGITONIN, 1 MM DTT；pH 7.6；30 MM HEPES/KOH 7.6, 10 MM MG(OAC)2, 180 MM KOAC/HAC PH 7.6, 0.3 % DIGITONIN, 1 MM DTT cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 95, INSTRUMENT- FEI VITROBOT MARK IV, METHOD- BLOT FOR 3 SECONDS BEFORE PLUNGING,	Resolution 7.80 Å
5A6U Native mammalian ribosome-bound Sec61 protein-conducting channel in the 'non-inserting' state Deposited 2015-07-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 61–96（36 aa） Fragment：UNP RESIDUES 61-96	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 20MM HEPES, 50MM KCL, 2MM MGCL2；pH 7.6；20MM HEPES, 50MM KCL, 2MM MGCL2 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；VITRIFICATION 1 -- CRYOGEN- ETHANE-PROPANE MIXTURE, HUMIDITY- 70, INSTRUMENT- FEI VITROBOT MARK IV, METHOD- BLOT 3 SECONDS BEFORE PLUNGING.,	Resolution 9.00 Å
6FTG Subtomogram average of OST-containing ribosome-translocon complexes from canine rough microsomal membranes Deposited 2018-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric	Chain z 68–96（29 aa）	Not recorded	MG MAGNESIUM ION × 159 ZN ZINC ION × 5 9UB [(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]methyl-[oxidanyl-[(2~{Z},6~{Z},10~{Z})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenoxy]phosphoryl]oxy-phosphinic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Blot 3 seconds before plunging.	Resolution 9.10 Å
6FTI Cryo-EM Structure of the Mammalian Oligosaccharyltransferase Bound to Sec61 and the Programmed 80S Ribosome Deposited 2018-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric	Chain z 68–96（29 aa）	Not recorded	MG MAGNESIUM ION × 159 ZN ZINC ION × 5 9UB [(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]methyl-[oxidanyl-[(2~{Z},6~{Z},10~{Z})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenoxy]phosphoryl]oxy-phosphinic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
6FTJ Cryo-EM Structure of the Mammalian Oligosaccharyltransferase Bound to Sec61 and the Non-programmed 80S Ribosome Deposited 2018-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric	Chain z 68–96（29 aa）	Not recorded	MG MAGNESIUM ION × 159 ZN ZINC ION × 5 9UB [(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]methyl-[oxidanyl-[(2~{Z},6~{Z},10~{Z})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenoxy]phosphoryl]oxy-phosphinic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.70 Å
6R7Q Structure of XBP1u-paused ribosome nascent chain complex with Sec61. Deposited 2019-03-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 88-meric	Chain ZZ 68–96（29 aa）	Not recorded	ZN ZINC ION × 6 MG MAGNESIUM ION × 299	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
7TM3 Structure of the rabbit 80S ribosome stalled on a 2-TMD Rhodopsin intermediate in complex with the multipass translocon Deposited 2022-01-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 54-meric	Chain 2 1–96（96 aa）	Not recorded	MG MAGNESIUM ION × 220 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50 mM HEPES-KOH, pH 7.5, 200 mM KOAc, 5 mM Mg(OAc)2, 0.25% digitonin, 50 mM biotin cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 sec with Whatman filter papers at a blot force of -15 before plunging	Resolution 3.25 Å
7TUT Structure of the rabbit 80S ribosome stalled on a 4-TMD Rhodopsin intermediate in complex with the multipass translocon Deposited 2022-02-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric	Chain 2 1–96（96 aa）	Not recorded	MG MAGNESIUM ION × 220 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50 mM HEPES-KOH, pH 7.5, 200 mM potassium acetate, 5 mM magnesium acetate, 0.25% digitonin, 50 mM biotin cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds with Whatman filter papers at a blot force of -15 before plunging.	Resolution 3.88 Å
8BTK Structure of the TRAP complex with the Sec translocon and a translating ribosome Deposited 2022-11-29	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 86 PDB declaration: 92-meric	Chain SZ 1–96（96 aa）	Not recorded	SPD SPERMIDINE × 30 SPM SPERMINE × 3 MG MAGNESIUM ION × 750 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 AAC ACETYLAMINO-ACETIC ACID × 1 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；3.5 uL of sample was incubated on the grid for 60 seconds at 4*C and 100% humidity before being blotted and plunged into liquid ethane/propane mix cooled to liquid nitrogen temperature	Resolution 3.50 Å
8RJB Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-RAMP4 Deposited 2023-12-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 51-meric	Chain 2 1–96（96 aa）	Not recorded	MG MAGNESIUM ION × 218 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.69 Å
8RJC Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 1 Deposited 2023-12-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric	Chain 2 1–96（96 aa）	Not recorded	MG MAGNESIUM ION × 218 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8RJD Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 2 Deposited 2023-12-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric	Chain 2 1–96（96 aa）	Not recorded	MG MAGNESIUM ION × 218 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.79 Å

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SC61B_CANFA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–96； UniProt 1–96

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2wwb
Deposition date deposition_date	2009-10-22
Structure title title	CRYO-EM STRUCTURE OF THE MAMMALIAN SEC61 COMPLEX BOUND TO THE ACTIVELY TRANSLATING WHEAT GERM 80S RIBOSOME
Keywords keywords	RIBOSOME, PROTEIN EXIT TUNNEL, COTRANSLATIONAL PROTEIN TRANSLOCATION, PROTEIN CONDUCTING CHANNEL, SIGNAL SEQUENCE; RIBOSOME
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	44.94 Å
Radius of gyration Rg (electron density) rg_electron	46.58 Å
Forward intensity I(0) i0	804995000.00
Molecular weight molecular_weight	206110.0 kDa
Excluded volume excluded_volume	247010 Å³
Envelope volume envelope_volume	407280 Å³
Hydration-shell volume shell_volume	74704 Å³
Envelope diameter envelope_diameter	170.2 Å
Shell Rg shell_rg	49.46 Å
Envelope Rg envelope_rg	45.81 Å
Shape Rg shape_rg	46.66 Å
Total Rg total_rg	46.48 Å
Total atoms total_atoms	14313
Residues n_residues	1591
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	154.9 Å
Rg (real space) rg_real	44.99 Å
Rg uncertainty (real space) rg_real_error	1.31 Å
I(0) (real space) i0_real	8.0500e+08
I(0) uncertainty (real space) i0_real_error	1.3130e+07
Rg (reciprocal space) rg_reciprocal	44.94 Å
I(0) (reciprocal space) i0_reciprocal	804900000.0000
Solution quality estimate total_estimate	0.8555
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	57.5 Å
Skewness Skewness skewness	0.428
Kurtosis Kurtosis kurtosis	0.013
Angular range angular_range	— – 0.1750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	49810000.0000
Real-space data points n_real_points	36
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.783; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.773

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (15)

Entity 1 Entity 1 polymer

Description description	PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 1
Molecular weight formula_weight	52279.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	14313

MAIKFLEVIKPFCVILPEIQKPERKIQFKEKVLWTAITLFIFLVCCQIPLFGIMSSDSADPFYWMRVILASNRGTLMELGISPIVTSGLIMQLLAGAKIIEVGDTPKDRALFNGAQKLFGMIITIGQSIVYVMTGMYGDPSEMGAGICLLITIQLFVAGLIVLLLDELLQKGYGLGSGISLFIATNICETIVWKAFSPTTVNTGRGMEFEGAIIALFHLLATRTDKVRALREAFYRQNLPNLMNLIATIFVFAVVIYFQGFRVDLPIKSARYRGQYNTYPIKLFYTSNIPIILQSALVSNLYVISQMLSARFSGNLLVSLLGTWSDTSSGGPARAYPVGGLCHYLSPPESFGSVLEDPVHAVVYIVFMLGSCAFFSKTWIEVSGSSAKDVAKQLKEQQMVMRGHRETSMVHELNRYIPTAAAFGGLCIGALSVLADFLGAIGSGTGILLAVTIIYQYFEIFVKEQSEVGSMGALLF

Entity 2 Entity 2 polymer

Description description	PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT GAMMA
Molecular weight formula_weight	7752.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MDQVMQFVEPSRQFVKDSIRLVKRCTKPDRKEFQKIAMATAIGFAIMGFIGFFVKLIHIPINNIIVGG

Entity 3 Entity 3 polymer

Description description	PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT BETA
Molecular weight formula_weight	9987.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MPGPTPSGTNVGSSGRSPSKAVAARAAGSTVRQRKNASCGTRSAGRTTSAGTGGMWRFYTEDSPGLKVGPVPVLVMSLLFIASVFMLHIWGKYTRS

Entity 4 Entity 4 polymer

Description description	5.8S RRNA
Molecular weight formula_weight	20302.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	D

AGAACGCAGCGAAAUGCGAUACGUAAUGUGAAUUGCAGAAUUCCGUGAAUCAUCGAAUCUUUG

Entity 5 Entity 5 polymer

Description description	25S RRNA
Molecular weight formula_weight	11089.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	E

UGAAAAGAACUUUGAAAAGAGAGUGAAAAAGUAC

Entity 6 Entity 6 polymer

Description description	25S RRNA
Molecular weight formula_weight	8052.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	F

CCACGUCAACAGCAGUUGGACGUGG

Entity 7 Entity 7 polymer

Description description	25S RRNA
Molecular weight formula_weight	4477.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	G

ACACGUCGCGCGGU

Entity 8 Entity 8 polymer

Description description	60S RIBOSOMAL PROTEIN L4-B
Molecular weight formula_weight	39129.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MSRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQTSAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRYATASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLKVLKSKKLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAPGAHLGRFVIWTEAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIRPAGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPAAVFAETLKHD

Entity 9 Entity 9 polymer

Description description	60S RIBOSOMAL PROTEIN L17-A
Molecular weight formula_weight	20589.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MARYGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQVLDHQRAIPFRRFNSSIGRTAQGKEFGVTKARWPAKSVKFVQGLLQNAAANAEAKGLDATKLYVSHIQVNQAPKQRRRTYRAHGRINKYESSPSHIELVVTEKEEAVAKAAEKKVVRLTSRQRGRIAAQKRIAA

Entity 10 Entity 10 polymer

Description description	60S RIBOSOMAL PROTEIN L19
Molecular weight formula_weight	21762.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

MANLRTQKRLAASVVGVGKRKVWLDPNETSEIAQANSRNAIRKLVKNGTIVKKAVTVHSKSRTRAHAQSKREGRHSGYGKRKGTREARLPSQVVWIRRLRVLRRLLAKYRDAGKIDKHLYHVLYKESKGNAFKHKRALVEHIIQAKADAQREKALNEEAEARRLKNRAARDRRAQRVAEKRDALLKEDA

Entity 11 Entity 11 polymer

Description description	60S RIBOSOMAL PROTEIN L25
Molecular weight formula_weight	15787.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MAPSAKATAAKKAVVKGTNGKKALKVRTSATFRLPKTLKLARAPKYASKAVPHYNRLDSYKVIEQPITSETAMKKVEDGNILVFQVSMKANKYQIKKAVKELYEVDVLKVNTLVRPNGTKKAYVRLTADYDALDIANRIGYI

Entity 12 Entity 12 polymer

Description description	60S RIBOSOMAL PROTEIN L26-A
Molecular weight formula_weight	14265.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MAKQSLDVSSDRRKARKAYFTAPSSQRRVLLSAPLSKELRAQYGIKALPIRRDDEVLVVRGSKKGQEGKISSVYRLKFAVQVDKVTKEKVNGASVPINLHPSKLVITKLHLDKDRKALIQRKGGKLE

Entity 13 Entity 13 polymer

Description description	60S RIBOSOMAL PROTEIN L31-A
Molecular weight formula_weight	12980.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MAGLKDVVTREYTINLHKRLHGVSFKKRAPRAVKEIKKFAKLHMGTDDVRLAPELNQAIWKRGVKGVEYRLRLRISRKRNEEEDAKNPLFSYVEPVLVASAKGLQTVVVEEDA

Entity 14 Entity 14 polymer

Description description	60S RIBOSOMAL PROTEIN L35
Molecular weight formula_weight	13942.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

MAGVKAYELRTKSKEQLASQLVDLKKELAELKVQKLSRPSLPKIKTVRKSIACVLTVINEQQREAVRQLYKGKKYQPKDLRAKKTRALRRALTKFEASQVTEKQRKKQIAFPQRKYAIKA

Entity 15 Entity 15 polymer

Description description	60S RIBOSOMAL PROTEIN L39
Molecular weight formula_weight	6358.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O

MAAQKSFRIKQKMAKAKKQNRPLPQWIRLRTNNTIRYNAKRRNWRRTKMNI

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	6.480 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	6.48 Å
Resolution测定方法 resolution_method	PROJECTION MATCHING
颗粒数 num_particles	221445

fit	/app/data/saxs_computation/ww/2wwb/2wwb.fit
pddf	/app/data/pr_computation/ww/2wwb/2wwb.pr.out
profile	/app/data/saxs_computation/ww/2wwb/2wwb.dat

CRYO-EM STRUCTURE OF THE MAMMALIAN SEC61 COMPLEX BOUND TO THE ACTIVELY TRANSLATING WHEAT GERM 80S RIBOSOME

1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 1

State in the Current Structure

Other States of the Same Protein in the Database

PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT GAMMA

State in the Current Structure

Other States of the Same Protein in the Database

PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT BETA

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (15)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 polymer

Polymer Polymer

Entity 9 Entity 9 polymer

Polymer Polymer

Entity 10 Entity 10 polymer

Polymer Polymer

Entity 11 Entity 11 polymer

Polymer Polymer

Entity 12 Entity 12 polymer

Polymer Polymer

Entity 13 Entity 13 polymer

Polymer Polymer

Entity 14 Entity 14 polymer

Polymer Polymer

Entity 15 Entity 15 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)