SAXSdb — 4bzk

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

Protein transport protein SEC31

Saccharomyces cerevisiae

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–1273 Chain C； UniProt 1–1273	Not recorded	Protein transport protein SEC13 × 1 （Q04491） Protein transport protein SEC13 × 1 （Q04491）	ELECTRON MICROSCOPY cryo-EM buffer：HEPES, 50 MM KOAC, 1.2 MM MGCL2；pH 6.8；HEPES, 50 MM KOAC, 1.2 MM MGCL2 cryo-EM vitrification conditions：Cryogen ETHANE；ETHANE; HOMEMADE PLUNGER	Resolution 40.00 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 4BZK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2PM6 Crystal Structure of yeast Sec13/31 edge element of the COPII vesicular coat, native version Deposited 2007-04-20	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 370–763（394 aa） Fragment：residues 370-763 Chain C 370–763（394 aa） Fragment：residues 370-763	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；15% PEG 4000, 10% DMSO, 6% dioxanie, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.45 Å R-free 0.301
2PM7 Crystal structure of yeast Sec13/31 edge element of the COPII vesicular coat, selenomethionine version Deposited 2007-04-20	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 370–763（394 aa） Fragment：residues 370-763 Chain C 370–763（394 aa） Fragment：residues 370-763	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；15% PEG 4000, 10% DMSO, 6% dioxane, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.35 Å R-free 0.298
2PM9 Crystal structure of yeast Sec13/31 vertex element of the COPII vesicular coat Deposited 2007-04-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–411（411 aa） Fragment：residues 1-411	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；295 K；8% PEG 3350, 0.1M tri-sodium citrate, 10mM manganese chloride, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.30 Å R-free 0.305
2QTV Structure of Sec23-Sar1 complexed with the active fragment of Sec31 Deposited 2007-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 899–947（49 aa） Fragment：residues 899-947	Not recorded	ZN ZINC ION × 1 MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；295 K；150 mM NaCl, 20 mM HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.262
3MZL Sec13/Sec31 edge element, loop deletion mutant Deposited 2010-05-12	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 370–473（104 aa） Fragment：UNP residues 370-746, deletion of residues 474-507 Chain B 508–746（239 aa） Fragment：UNP residues 370-746, deletion of residues 474-507 Chain D 370–473（104 aa） Fragment：UNP residues 370-746, deletion of residues 474-507 Chain D 508–746（239 aa） Fragment：UNP residues 370-746, deletion of residues 474-507	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；289 K；0.1mM bis-Tris propane, 0.2M sodium citrate, 16% polyethylene glycol 3350, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.80 Å R-free 0.300
3MZL Sec13/Sec31 edge element, loop deletion mutant Deposited 2010-05-12	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 370–473（104 aa） Fragment：UNP residues 370-746, deletion of residues 474-507 Chain F 508–746（239 aa） Fragment：UNP residues 370-746, deletion of residues 474-507 Chain H 370–473（104 aa） Fragment：UNP residues 370-746, deletion of residues 474-507 Chain H 508–746（239 aa） Fragment：UNP residues 370-746, deletion of residues 474-507	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；289 K；0.1mM bis-Tris propane, 0.2M sodium citrate, 16% polyethylene glycol 3350, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.80 Å R-free 0.300
4BZJ The structure of the COPII coat assembled on membranes Deposited 2013-07-26	Parsed fields agree	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–1273（1273 aa） Chain C 1–1273（1273 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer HEPES, 50 MM KOAC, 1.2 MM MGCL2；pH 6.8；HEPES, 50 MM KOAC, 1.2 MM MGCL2 cryo-EM vitrification conditions Cryogen ETHANE；ETHANE; HOMEMADE PLUNGER	Resolution 40.00 Å
6ZG5 COPII on membranes, outer coat right-handed rod, class1 Deposited 2020-06-18	Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–1273（1273 aa） Chain C 1–1273（1273 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 40.00 Å
6ZG6 COPII on membranes, outer coat vertex Deposited 2020-06-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–1273（1273 aa） Chain C 1–1273（1273 aa） Chain E 1–1273（1273 aa） Chain G 1–1273（1273 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 12.00 Å
6ZL0 COPII on membranes, outer coat left-handed rod Deposited 2020-06-30	Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–1273（1273 aa） Chain C 1–1273（1273 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 40.00 Å

9 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SEC31_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1273； UniProt 1–1273 Author chain C； PDBConstruct 1–1273； UniProt 1–1273

Protein transport protein SEC13

Saccharomyces cerevisiae

UniProt Q04491

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1–297 Chain F； UniProt 1–297	Not recorded	Protein transport protein SEC31 × 2 （P38968）	ELECTRON MICROSCOPY cryo-EM buffer：HEPES, 50 MM KOAC, 1.2 MM MGCL2；pH 6.8；HEPES, 50 MM KOAC, 1.2 MM MGCL2 cryo-EM vitrification conditions：Cryogen ETHANE；ETHANE; HOMEMADE PLUNGER	Resolution 40.00 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 4BZK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2PM6 Crystal Structure of yeast Sec13/31 edge element of the COPII vesicular coat, native version Deposited 2007-04-20	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–297（297 aa） Chain D 1–297（297 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；15% PEG 4000, 10% DMSO, 6% dioxanie, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.45 Å R-free 0.301
2PM7 Crystal structure of yeast Sec13/31 edge element of the COPII vesicular coat, selenomethionine version Deposited 2007-04-20	Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–297（297 aa） Chain D 1–297（297 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；15% PEG 4000, 10% DMSO, 6% dioxane, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.35 Å R-free 0.298
2PM9 Crystal structure of yeast Sec13/31 vertex element of the COPII vesicular coat Deposited 2007-04-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–297（297 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；295 K；8% PEG 3350, 0.1M tri-sodium citrate, 10mM manganese chloride, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.30 Å R-free 0.305
3IKO Crystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucleoporin complex Deposited 2009-08-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–297（297 aa） Fragment：UNP residues 1-297	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 20000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.20 Å R-free 0.273
3IKO Crystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucleoporin complex Deposited 2009-08-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–297（297 aa） Fragment：UNP residues 1-297	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 20000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.20 Å R-free 0.273
3IKO Crystal structure of the heterotrimeric Sec13-Nup145C-Nup84 nucleoporin complex Deposited 2009-08-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–297（297 aa） Fragment：UNP residues 1-297	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 20000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.20 Å R-free 0.273
3JRO NUP84-NUP145C-SEC13 edge element of the NPC lattice Deposited 2009-09-08	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–297（297 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；295 K；1.15M sodium malonate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 4.00 Å R-free 0.329
3JRP SEC13 with NUP145C (AA109-179) insertion blade Deposited 2009-09-08	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–297（297 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；289 K；0.1M Tris, 22% PEG 4000, 0.25 M LiCl, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.60 Å R-free 0.254
3MZK Sec13/Sec16 complex, S.cerevisiae Deposited 2010-05-12	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–297（297 aa） Chain D 1–297（297 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.1mM bis-Tris propane, 0.2M NaBr, 12% polyethylene glycol 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.69 Å R-free 0.243
3MZL Sec13/Sec31 edge element, loop deletion mutant Deposited 2010-05-12	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–297（297 aa） Chain C 1–297（297 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；289 K；0.1mM bis-Tris propane, 0.2M sodium citrate, 16% polyethylene glycol 3350, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.80 Å R-free 0.300
3MZL Sec13/Sec31 edge element, loop deletion mutant Deposited 2010-05-12	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–297（297 aa） Chain G 1–297（297 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；289 K；0.1mM bis-Tris propane, 0.2M sodium citrate, 16% polyethylene glycol 3350, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.80 Å R-free 0.300
4BZJ The structure of the COPII coat assembled on membranes Deposited 2013-07-26	Different construct	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 2–292（291 aa） Chain F 2–292（291 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer HEPES, 50 MM KOAC, 1.2 MM MGCL2；pH 6.8；HEPES, 50 MM KOAC, 1.2 MM MGCL2 cryo-EM vitrification conditions Cryogen ETHANE；ETHANE; HOMEMADE PLUNGER	Resolution 40.00 Å
4XMM Structure of the yeast coat nucleoporin complex, space group C2 Deposited 2015-01-14	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–297（297 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；PEG 20000, ethanol, MES	Resolution 7.38 Å R-free 0.353
4XMN Structure of the yeast coat nucleoporin complex, space group P212121 Deposited 2015-01-14	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 2–297（296 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；PEG 20000, ethanol, MES	Resolution 7.60 Å R-free 0.347
6ZG5 COPII on membranes, outer coat right-handed rod, class1 Deposited 2020-06-18	Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–297（297 aa） Chain F 1–297（297 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 40.00 Å
6ZG6 COPII on membranes, outer coat vertex Deposited 2020-06-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–297（297 aa） Chain D 1–297（297 aa） Chain F 1–297（297 aa） Chain H 1–297（297 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 12.00 Å
6ZL0 COPII on membranes, outer coat left-handed rod Deposited 2020-06-30	Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–297（297 aa） Chain D 1–297（297 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 40.00 Å
7N84 Double nuclear outer ring from the isolated yeast NPC Deposited 2021-06-13	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 136 PDB declaration: 136-meric	Chain d 1–297（297 aa） Chain o 1–297（297 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 11.60 Å
7N84 Double nuclear outer ring from the isolated yeast NPC Deposited 2021-06-13	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain d 1–297（297 aa） Chain o 1–297（297 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 11.60 Å
7N84 Double nuclear outer ring from the isolated yeast NPC Deposited 2021-06-13	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain d 1–297（297 aa） Chain o 1–297（297 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 11.60 Å
7N9F Structure of the in situ yeast NPC Deposited 2021-06-17	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 448 PDB declaration: 448-meric	Chain d 1–297（297 aa） Chain k 1–297（297 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；A custom-built vitrification device (Max Planck Institute for Biochemistry, Munich)	Resolution 37.00 Å
7N9F Structure of the in situ yeast NPC Deposited 2021-06-17	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric	Chain d 1–297（297 aa） Chain k 1–297（297 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；A custom-built vitrification device (Max Planck Institute for Biochemistry, Munich)	Resolution 37.00 Å
7N9F Structure of the in situ yeast NPC Deposited 2021-06-17	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 56 PDB declaration: 56-meric	Chain d 1–297（297 aa） Chain k 1–297（297 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；A custom-built vitrification device (Max Planck Institute for Biochemistry, Munich)	Resolution 37.00 Å
8ADL Cryo-EM structure of the SEA complex Deposited 2022-07-08	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 22 PDB declaration: 22-meric	Chain H 1–297（297 aa） Chain P 1–297（297 aa）	Not recorded	ZN ZINC ION × 28	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.95 Å
8TIE Double nuclear outer ring of Nup84-complexes from the yeast NPC Deposited 2023-07-19	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain d 1–297（297 aa） Chain o 1–297（297 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20mM HEPES,50mM Potassium acetate,20mM NaCl,2mM MgCl2,1mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.10 Å
9H5K Cryo-EM structure of the SEAC-EGOC supercomplex Deposited 2024-10-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain H 1–297（297 aa） Chain P 1–297（297 aa）	Not recorded	ZN ZINC ION × 28 MG MAGNESIUM ION × 2 AF3 ALUMINUM FLUORIDE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å

19 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SEC13_YEAST
Isoform	—
PDB entities	2, 3
Chains and sequence ranges	Author chain B； PDBConstruct 1–297； UniProt 1–297 Author chain F； PDBConstruct 1–297； UniProt 1–297

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4bzk
Deposition date deposition_date	2013-07-26
Structure title title	The structure of the COPII coat assembled on membranes
Keywords keywords	PROTEIN TRANSPORT, SECRETION, TRAFFICKING; PROTEIN TRANSPORT
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	93.73 Å
Radius of gyration Rg (electron density) rg_electron	96.32 Å
Forward intensity I(0) i0	661602000.00
Molecular weight molecular_weight	215820.0 kDa
Excluded volume excluded_volume	269530 Å³
Envelope volume envelope_volume	440840 Å³
Hydration-shell volume shell_volume	47789 Å³
Envelope diameter envelope_diameter	301.4 Å
Shell Rg shell_rg	53.68 Å
Envelope Rg envelope_rg	93.25 Å
Shape Rg shape_rg	96.36 Å
Total Rg total_rg	95.47 Å
Total atoms total_atoms	15238
Residues n_residues	1943
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	251.0 Å
Rg (real space) rg_real	88.47 Å
Rg uncertainty (real space) rg_real_error	1.51 Å
I(0) (real space) i0_real	6.3630e+08
I(0) uncertainty (real space) i0_real_error	1.3040e+07
Rg (reciprocal space) rg_reciprocal	82.59 Å
I(0) (reciprocal space) i0_reciprocal	639400000.0000
Solution quality estimate total_estimate	0.6273
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	29.5 Å
Skewness Skewness skewness	0.375
Kurtosis Kurtosis kurtosis	-1.144
Angular range angular_range	— – 0.0850 Å⁻¹
Current regularization parameter α current_alpha	0.2430
Highest regularization parameter α highest_alpha	9972000.0000
Real-space data points n_real_points	18
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.116; Stabil: 0.904; Sysdev: 1.000; Positv: 1.000; Valcen: 0.095; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Protein transport protein SEC31
Molecular weight formula_weight	138833.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	15423

MVKLAEFSRTATFAWSHDKIPLLVSGTVSGTVDANFSTDSSLELWSLLAADSEKPIASLQVDSKFNDLDWSHNNKIIAGALDNGSLELYSTNEANNAINSMARFSNHSSSVKTVKFNAKQDNVLASGGNNGEIFIWDMNKCTESPSNYTPLTPGQSMSSVDEVISLAWNQSLAHVFASAGSSNFASIWDLKAKKEVIHLSYTSPNSGIKQQLSVVEWHPKNSTRVATATGSDNDPSILIWDLRNANTPLQTLNQGHQKGILSLDWCHQDEHLLLSSGRDNTVLLWNPESAEQLSQFPARGNWCFKTKFAPEAPDLFACASFDNKIEVQTLQNLTNTLDEQETETKQQESETDFWNNVSREESKEKPSVFHLQAPTWYGEPSPAAHWAFGGKLVQITPDGKGVSITNPKISGLESNTTLSEALKTKDFKPLINQRLVKVIDDVNEEDWNLLEKLSMDGTEEFLKEALAFDNDESDAQDDANNEKEDDGEEFFQQIETNFQPEGDFSLSGNIEQTISKNLVSGNIKSAVKNSLENDLLMEAMVIALDSNNERLKESVKNAYFAKYGSKSSLSRILYSISKREVDDLVENLDVSQWKFISKAIQNLYPNDIAQRNEMLIKLGDRLKENGHRQDSLTLYLAAGSLDKVASIWLSEFPDLEDKLKKDNKTIYEAHSECLTEFIERFTVFSNFINGSSTINNEQLIAKFLEFINLTTSTGNFELATEFLNSLPSDNEEVKTEKARVLIASGKSLPAQNPATATTSKAKYTNAKTNKNVPVLPTPGMPSTTSIPSMQAPFYGMTPGASANALPPKPYVPATTTSAPVHTEGKYAPPSQPSMASPFVNKTNSSTRLNSFAPPPNPYATATVPATNVSTTSIPQNTFAPIQPGMPIMGDYNAQSSSIPSQPPINAVSGQTPHLNRKANDGWNDLPLKVKEKPSRAKAVSVAPPNILSTPTPLNGIPANAASTMPPPPLSRAPSSVSMVSPPPLHKNSRVPSLVATSESPRASISNPYAPPQSSQQFPIGTISTANQTSNTAQVASSNPYAPPPQQRVATPLSGGVPPAPLPKASNPYAPTATTQPNGSSYPPTGPYTNNHTMTSPPPVFNKPPTGPPPISMKKRSNKLASIEQNPSQGATYPPTLSSSASPLQPSQPPTLASQVNTSAENVSHEIPADQQPIVDFLKEELARVTPLTPKEYSKQLKDCDKRLKILFYHLEKQDLLTQPTIDCLHDLVALMKEKKYKEAMVIHANIATNHAQEGGNWLTGVKRLIGIAEATLN

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	SACCHAROMYCES CEREVISIAE

Entity 2 Entity 2 polymer

Description description	Protein transport protein SEC13
Molecular weight formula_weight	33083.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MVVIANAHNELIHDAVLDYYGKRLATCSSDKTIKIFEVEGETHKLIDTLTGHEGPVWRVDWAHPKFGTILASCSYDGKVLIWKEENGRWSQIAVHAVHSASVNSVQWAPHEYGPLLLVASSDGKVSVVEFKENGTTSPIIIDAHAIGVNSASWAPATIEEDGEHNGTKESRKFVTGGADNLVKIWKYNSDAQTYVLESTLEGHSDWVRDVAWSPTVLLRSYLASVSQDRTCIIWTQDNEQGPWKKTLLKEEKFPDVLWRASWSLSGNVLALSGGDNKVTLWKENLEGKWEPAGEVHQ

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	SACCHAROMYCES CEREVISIAE

Entity 3 Entity 3 polymer

Description description	Protein transport protein SEC13
Molecular weight formula_weight	33191.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MVVIANAHNEMIHDAVMDYYGKRMATCSSDKTIKIFEVEGETHKLIDTLTGHEGPVWRVDWAHPKFGTILASCSYDGKVMIWKEENGRWSQIAVHAVHSASVNSVQWAPHEYGPMLLVASSDGKVSVVEFKENGTTSPIIIDAHAIGVNSASWAPATIEEDGEHNGTKESRKFVTGGADNLVKIWKYNSDAQTYVLESTLEGHSDWVRDVAWSPTVLLRSYMASVSQDRTCIIWTQDNEQGPWKKTLLKEEKFPDVLWRASWSLSGNVLALSGGDNKVTLWKENLEGKWEPAGEVHQ

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	SACCHAROMYCES CEREVISIAE

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	185

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

Resolution resolution	40.00 Å
Resolution测定方法 resolution_method	SUBTOMOGRAM ALIGNMENT AND AVERAGING
颗粒数 num_particles	192

fit	/app/data/saxs_computation/bz/4bzk/4bzk.fit
pddf	/app/data/pr_computation/bz/4bzk/4bzk.pr.out
profile	/app/data/saxs_computation/bz/4bzk/4bzk.dat

The structure of the COPII coat assembled on membranes

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

Protein transport protein SEC31

State in the Current Structure

Other States of the Same Protein in the Database

Protein transport protein SEC13

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)