3mzl

Sec13/Sec31 edge element, loop deletion mutant

Method: X-RAY DIFFRACTION D_max: 225.9 Å Quality: GOOD

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

Protein transport protein SEC13

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 1–297 Chain C； UniProt 1–297	Not recorded	Protein transport protein SEC31 × 2 （P38968）	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
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 1–297 Chain G； UniProt 1–297	Not recorded	Protein transport protein SEC31 × 2 （P38968）	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

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 3MZL	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 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 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 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 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 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 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 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 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 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
4BZJ The structure of the COPII coat assembled on membranes Deposited 2013-07-26	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	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
4BZK The structure of the COPII coat assembled on membranes Deposited 2013-07-26	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 F 1–297（297 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 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 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 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 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 method 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 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	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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SEC13_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–297； UniProt 1–297 Author chain C； PDBConstruct 1–297； UniProt 1–297 Author chain E； PDBConstruct 1–297； UniProt 1–297 Author chain G； PDBConstruct 1–297； UniProt 1–297

Protein transport protein SEC31

Saccharomyces cerevisiae

UniProt P38968

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 370–473 Chain B； UniProt 508–746 Chain D； UniProt 370–473 Chain D； UniProt 508–746	Fragment：UNP residues 370-746, deletion of residues 474-507	Protein transport protein SEC13 × 2 （Q04491）	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
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain F； UniProt 370–473 Chain F； UniProt 508–746 Chain H； UniProt 370–473 Chain H； UniProt 508–746	Fragment：UNP residues 370-746, deletion of residues 474-507	Protein transport protein SEC13 × 2 （Q04491）	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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 3MZL	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 mutation/modification 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 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 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 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
4BZJ The structure of the COPII coat assembled on membranes Deposited 2013-07-26	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 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
4BZK The structure of the COPII coat assembled on membranes Deposited 2013-07-26	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 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 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 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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–1273（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 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 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 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SEC31_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–106； UniProt 370–473 Author chain B； PDBConstruct 107–345； UniProt 508–746 Author chain D； PDBConstruct 3–106； UniProt 370–473 Author chain D； PDBConstruct 107–345； UniProt 508–746 Author chain F； PDBConstruct 3–106； UniProt 370–473 Author chain F； PDBConstruct 107–345； UniProt 508–746 Author chain H； PDBConstruct 3–106； UniProt 370–473 Author chain H； PDBConstruct 107–345； UniProt 508–746

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	3mzl
Deposition date deposition_date	2010-05-12
Structure title title	Sec13/Sec31 edge element, loop deletion mutant
Keywords keywords	alpha-helical-stack, beta-propeller, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	86.83 Å
Radius of gyration Rg (electron density) rg_electron	88.43 Å
Forward intensity I(0) i0	1008570000.00
Molecular weight molecular_weight	271870.0 kDa
Excluded volume excluded_volume	341720 Å³
Envelope volume envelope_volume	628290 Å³
Hydration-shell volume shell_volume	70416 Å³
Envelope diameter envelope_diameter	293.5 Å
Shell Rg shell_rg	65.52 Å
Envelope Rg envelope_rg	84.50 Å
Shape Rg shape_rg	88.49 Å
Total Rg total_rg	87.80 Å
Total atoms total_atoms	19212
Residues n_residues	2432
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	225.9 Å
Rg (real space) rg_real	80.66 Å
Rg uncertainty (real space) rg_real_error	1.14 Å
I(0) (real space) i0_real	9.6350e+08
I(0) uncertainty (real space) i0_real_error	1.7640e+07
Rg (reciprocal space) rg_reciprocal	81.65 Å
I(0) (reciprocal space) i0_reciprocal	993400000.0000
Solution quality estimate total_estimate	0.8615
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	75.3 Å
Skewness Skewness skewness	0.191
Kurtosis Kurtosis kurtosis	-1.013
Angular range angular_range	— – 0.0900 Å⁻¹
Current regularization parameter α current_alpha	0.5943
Highest regularization parameter α highest_alpha	19240000.0000
Real-space data points n_real_points	19
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.001; Oscil: 0.924; Stabil: 0.985; Sysdev: 1.000; Positv: 1.000; Valcen: 0.471; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Protein transport protein SEC13
Molecular weight formula_weight	33083.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	19212

MVVIANAHNELIHDAVLDYYGKRLATCSSDKTIKIFEVEGETHKLIDTLTGHEGPVWRVDWAHPKFGTILASCSYDGKVLIWKEENGRWSQIAVHAVHSASVNSVQWAPHEYGPLLLVASSDGKVSVVEFKENGTTSPIIIDAHAIGVNSASWAPATIEEDGEHNGTKESRKFVTGGADNLVKIWKYNSDAQTYVLESTLEGHSDWVRDVAWSPTVLLRSYLASVSQDRTCIIWTQDNEQGPWKKTLLKEEKFPDVLWRASWSLSGNVLALSGGDNKVTLWKENLEGKWEPAGEVHQ

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	yeast
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Protein transport protein SEC31
Molecular weight formula_weight	38692.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

GPHLQAPTWYGEPSPAAHWAFGGKLVQITPDGKGVSITNPKISGLESNTTLSEALKTKDFKPLINQRLVKVIDDVNEEDWNLLEKLSMDGTEEFLKEALAFDNDESGNIEQTISKNLVSGNIKSAVKNSLENDLLMEAMVIALDSNNERLKESVKNAYFAKYGSKSSLSRILYSISKREVDDLVENLDVSQWKFISKAIQNLYPNDIAQRNEMLIKLGDRLKENGHRQDSLTLYLAAGSLDKVASIWLSEFPDLEDKLKKDNKTIYEAHSECLTEFIERFTVFSNFINGSSTINNEQLIAKFLEFINLTTSTGNFELATEFLNSLPSDNEEVKTEKARVLIASGK

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	yeast
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

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7. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	3mzlA01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	3mzlB01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	400 —

Domain ID domain_id	3mzlB02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1600 —

Domain ID domain_id	3mzlB03
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	980 —

Domain ID domain_id	3mzlC01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	3mzlD01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	400 —

Domain ID domain_id	3mzlD02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1600 —

Domain ID domain_id	3mzlD03
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	980 —

Domain ID domain_id	3mzlE01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	3mzlF01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	400 —

Domain ID domain_id	3mzlF02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1600 —

Domain ID domain_id	3mzlF03
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	980 —

Domain ID domain_id	3mzlG01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	3mzlH01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	400 —

Domain ID domain_id	3mzlH02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1600 —

Domain ID domain_id	3mzlH03
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	980 —

▶

8. Citations (1)

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Unit-cell length a length_a	156.220 Å
Unit-cell length b length_b	46.620 Å
Unit-cell length c length_c	192.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.48 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	29.380 Å
R factor r_factor	0.2680
R_work r_work	0.2671
R_free r_free	0.2996

fit	/app/data/saxs_computation/mz/3mzl/3mzl.fit
pddf	/app/data/pr_computation/mz/3mzl/3mzl.pr.out
profile	/app/data/saxs_computation/mz/3mzl/3mzl.dat

Sec13/Sec31 edge element, loop deletion mutant

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

Protein transport protein SEC13

State in the Current Structure

Other States of the Same Protein in the Database

Protein transport protein SEC31

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

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)