SAXSdb — 1cr5

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

SEC18P (RESIDUES 22 - 210)

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 22–210	Fragment：N-TERMINAL DOMAIN	NEN 1-ETHYL-PYRROLIDINE-2,5-DIONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；PEG 8000, sodium phosphate, dimethyl sulfoxide, ATP, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 2.30 Å R-free 0.277
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 22–210	Fragment：N-TERMINAL DOMAIN	NEN 1-ETHYL-PYRROLIDINE-2,5-DIONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；PEG 8000, sodium phosphate, dimethyl sulfoxide, ATP, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 2.30 Å R-free 0.277
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 22–210	Fragment：N-TERMINAL DOMAIN	NEN 1-ETHYL-PYRROLIDINE-2,5-DIONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；PEG 8000, sodium phosphate, dimethyl sulfoxide, ATP, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 2.30 Å R-free 0.277

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 1CR5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9CRU Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 1 Deposited 2024-07-22	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 × 11 PDB declaration: undecameric	Chain A 1–758（758 aa） Chain B 1–758（758 aa） Chain C 1–758（758 aa） Chain D 1–758（758 aa） Chain E 1–758（758 aa） Chain F 1–758（758 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.89 Å
9CRX Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 3 Deposited 2024-07-22	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 × 12 PDB declaration: dodecameric	Chain A 1–758（758 aa） Chain B 1–758（758 aa） Chain C 1–758（758 aa） Chain D 1–758（758 aa） Chain E 1–758（758 aa） Chain F 1–758（758 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.73 Å
9N22 Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 2 Deposited 2025-01-27	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 × 12 PDB declaration: dodecameric	Chain A 1–758（758 aa） Chain B 1–758（758 aa） Chain C 1–758（758 aa） Chain D 1–758（758 aa） Chain E 1–758（758 aa） Chain F 1–758（758 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.91 Å
9NG2 Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 4 Deposited 2025-02-21	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 × 12 PDB declaration: dodecameric	Chain A 1–758（758 aa） Chain B 1–758（758 aa） Chain C 1–758（758 aa） Chain D 1–758（758 aa） Chain E 1–758（758 aa） Chain F 1–758（758 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.61 Å
9NLU Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 5 Deposited 2025-03-03	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 × 12 PDB declaration: dodecameric	Chain A 1–758（758 aa） Chain B 1–758（758 aa） Chain C 1–758（758 aa） Chain D 1–758（758 aa） Chain E 1–758（758 aa） Chain F 1–758（758 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.29 Å
9NLW Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 6 Deposited 2025-03-03	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 × 12 PDB declaration: dodecameric	Chain A 1–758（758 aa） Chain B 1–758（758 aa） Chain C 1–758（758 aa） Chain D 1–758（758 aa） Chain E 1–758（758 aa） Chain F 1–758（758 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.73 Å
9NLY Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 7 Deposited 2025-03-03	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 × 12 PDB declaration: dodecameric	Chain A 1–758（758 aa） Chain B 1–758（758 aa） Chain C 1–758（758 aa） Chain D 1–758（758 aa） Chain E 1–758（758 aa） Chain F 1–758（758 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.75 Å
9NLZ Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 8 Deposited 2025-03-03	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 × 12 PDB declaration: dodecameric	Chain A 1–758（758 aa） Chain B 1–758（758 aa） Chain C 1–758（758 aa） Chain D 1–758（758 aa） Chain E 1–758（758 aa） Chain F 1–758（758 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.13 Å
9NM1 Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - All Merge (Class 9, focused on D1/D2) Deposited 2025-03-03	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 × 7 PDB declaration: heptameric	Chain A 1–758（758 aa） Chain B 1–758（758 aa） Chain C 1–758（758 aa） Chain D 1–758（758 aa） Chain E 1–758（758 aa） Chain F 1–758（758 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9NUD Y20S after Mg2+ (Sec18) - Class 2 Deposited 2025-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–758（758 aa） Chain B 1–758（758 aa） Chain C 1–758（758 aa） Chain D 1–758（758 aa） Chain E 1–758（758 aa） Chain F 1–758（758 aa）	Not recorded	MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.38 Å
9NUE Y20S after Mg2+ (Sec18) - Class 3 Deposited 2025-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain A 1–758（758 aa） Chain B 1–758（758 aa） Chain C 1–758（758 aa） Chain D 1–758（758 aa） Chain E 1–758（758 aa） Chain F 1–758（758 aa） Chain G 1–758（758 aa）	Not recorded	MG MAGNESIUM ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.36 Å
9NUZ Y20S after Mg2+ (Sec18) - Class 4 Deposited 2025-03-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain A 1–758（758 aa） Chain B 1–758（758 aa） Chain C 1–758（758 aa） Chain D 1–758（758 aa） Chain E 1–758（758 aa） Chain F 1–758（758 aa） Chain G 1–758（758 aa）	Not recorded	MG MAGNESIUM ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ATP ADENOSINE-5'-TRIPHOSPHATE × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å
9NV0 Sec18 Mg2+ class 2 Deposited 2025-03-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–758（758 aa） Chain B 1–758（758 aa） Chain C 1–758（758 aa） Chain D 1–758（758 aa） Chain E 1–758（758 aa） Chain F 1–758（758 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.83 Å
9NV1 Sec18 Mg2+ class 1 Deposited 2025-03-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain A 1–758（758 aa） Chain B 1–758（758 aa） Chain C 1–758（758 aa） Chain D 1–758（758 aa） Chain E 1–758（758 aa） Chain F 1–758（758 aa） Chain G 1–758（758 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 7 ATP ADENOSINE-5'-TRIPHOSPHATE × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.99 Å

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

View Construct and Data Evidence

UniProt name	SEC18_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–189； UniProt 22–210 Author chain B； PDBConstruct 1–189； UniProt 22–210 Author chain C； PDBConstruct 1–189； UniProt 22–210

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	1cr5
Deposition date deposition_date	1999-08-13
Structure title title	N-TERMINAL DOMAIN OF SEC18P
Keywords keywords	DOUBLE-PSI BETA BARREL, VESICLE FUSION, ENDOCYTOSIS-EXOCYTOSIS COMPLEX; ENDOCYTOSIS/EXOCYTOSIS
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	33.10 Å
Radius of gyration Rg (electron density) rg_electron	32.30 Å
Forward intensity I(0) i0	57044600.00
Molecular weight molecular_weight	60519.0 kDa
Excluded volume excluded_volume	75933 Å³
Envelope volume envelope_volume	102050 Å³
Hydration-shell volume shell_volume	26484 Å³
Envelope diameter envelope_diameter	104.2 Å
Shell Rg shell_rg	39.10 Å
Envelope Rg envelope_rg	31.24 Å
Shape Rg shape_rg	32.29 Å
Total Rg total_rg	32.93 Å
Total atoms total_atoms	4285
Residues n_residues	529
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	98.5 Å
Rg (real space) rg_real	32.99 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	5.7040e+07
I(0) uncertainty (real space) i0_real_error	8.3770e+05
Rg (reciprocal space) rg_reciprocal	33.04 Å
I(0) (reciprocal space) i0_reciprocal	57050000.0000
Solution quality estimate total_estimate	0.8779
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	53.4 Å
Skewness Skewness skewness	-0.016
Kurtosis Kurtosis kurtosis	-0.894
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5881000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.868; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.945; Smooth: 0.861

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	SEC18P (RESIDUES 22 - 210)
Molecular weight formula_weight	21324.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	4555

MDTRTRHLKVSNCPNNSYALANVAAVSPNDFPNNIYIIIDNLFVFTTRHSNDIPPGTIGFNGNQRTWGGWSLNQDVQAKAFDLFKYSGKQSYLGSIDIDISFRARGKAVSTVFDQDELAKQFVRCYESQIFSPTQYLIMEFQGHFFDLKIRNVQAIDLGDIEPTSAVATGIETKGILTKQTQINFFKGR

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	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1-ETHYL-PYRROLIDINE-2,5-DIONE
Molecular weight formula_weight	127.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	270

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1cr5a1
Class class	b — All beta proteins
Fold Fold fold	b.52 — Double psi beta-barrel
Superfamily Superfamily superfamily	b.52.2 — ADC-like
Family Family family	b.52.2.3 — Cdc48 N-terminal domain-like

Domain ID domain_id	d1cr5a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.31 — Cdc48 domain 2-like
Superfamily Superfamily superfamily	d.31.1 — Cdc48 domain 2-like
Family Family family	d.31.1.1 — Cdc48 domain 2-like

Domain ID domain_id	d1cr5b1
Class class	b — All beta proteins
Fold Fold fold	b.52 — Double psi beta-barrel
Superfamily Superfamily superfamily	b.52.2 — ADC-like
Family Family family	b.52.2.3 — Cdc48 N-terminal domain-like

Domain ID domain_id	d1cr5b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.31 — Cdc48 domain 2-like
Superfamily Superfamily superfamily	d.31.1 — Cdc48 domain 2-like
Family Family family	d.31.1.1 — Cdc48 domain 2-like

Domain ID domain_id	d1cr5c1
Class class	b — All beta proteins
Fold Fold fold	b.52 — Double psi beta-barrel
Superfamily Superfamily superfamily	b.52.2 — ADC-like
Family Family family	b.52.2.3 — Cdc48 N-terminal domain-like

Domain ID domain_id	d1cr5c2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.31 — Cdc48 domain 2-like
Superfamily Superfamily superfamily	d.31.1 — Cdc48 domain 2-like
Family Family family	d.31.1.1 — Cdc48 domain 2-like

CATH v4.4 (6 domains)

Domain ID domain_id	1cr5A01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1cr5A02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	330 — Vcp-like ATPase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1cr5B01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1cr5B02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	330 — Vcp-like ATPase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1cr5C01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1cr5C02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	330 — Vcp-like ATPase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	93.710 Å
Unit-cell length b length_b	32.140 Å
Unit-cell length c length_c	94.850 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	118.70 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2300
R_free r_free	0.2770

fit	/app/data/saxs_computation/cr/1cr5/1cr5.fit
pddf	/app/data/pr_computation/cr/1cr5/1cr5.pr.out
profile	/app/data/saxs_computation/cr/1cr5/1cr5.dat

N-TERMINAL DOMAIN OF SEC18P

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

SEC18P (RESIDUES 22 - 210)

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