SAXSdb — 9z5n

▼

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

Major vault protein

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 homooligomer Homooligomer Protein × 39 PDB declaration: 39-meric（39） Consistent with protein copy count	Chain A； UniProt 751–890 Chain B； UniProt 751–890 Chain C； UniProt 751–890 Chain D； UniProt 751–890 Chain E； UniProt 751–890 Chain F； UniProt 751–890 Chain G； UniProt 751–890 Chain H； UniProt 751–890 Chain I； UniProt 751–890 Chain J； UniProt 751–890 Chain K； UniProt 751–890 Chain L； UniProt 751–890 Chain M； UniProt 751–890 Chain N； UniProt 751–890 Chain O； UniProt 751–890 Chain P； UniProt 751–890 Chain Q； UniProt 751–890 Chain R； UniProt 751–890 Chain S； UniProt 751–890 Chain T； UniProt 751–890 Chain U； UniProt 751–890 Chain V； UniProt 751–890 Chain W； UniProt 751–890 Chain X； UniProt 751–890 Chain Y； UniProt 751–890 Chain Z； UniProt 751–890 Chain a； UniProt 751–890 Chain b； UniProt 751–890 Chain c； UniProt 751–890 Chain d； UniProt 751–890 Chain e； UniProt 751–890 Chain f； UniProt 751–890 Chain g； UniProt 751–890 Chain h； UniProt 751–890 Chain i； UniProt 751–890 Chain j； UniProt 751–890 Chain k； UniProt 751–890 Chain l； UniProt 751–890 Chain m； UniProt 751–890	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 6.8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.25 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 9Z5N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9Z4W Cryo-EM structure of rabbit major vault protein complex Deposited 2025-11-11	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 78 PDB declaration: 78-meric	Chain 0 1–890（890 aa） Chain 1 1–890（890 aa） Chain 2 1–890（890 aa） Chain 3 1–890（890 aa） Chain 4 1–890（890 aa） Chain 5 1–890（890 aa） Chain 6 1–890（890 aa） Chain 7 1–890（890 aa） Chain 8 1–890（890 aa） Chain 9 1–890（890 aa） Chain A 1–890（890 aa） Chain AA 1–890（890 aa） Chain AB 1–890（890 aa） Chain AC 1–890（890 aa） Chain AD 1–890（890 aa） Chain AE 1–890（890 aa） Chain AF 1–890（890 aa） Chain AG 1–890（890 aa） Chain AH 1–890（890 aa） Chain AI 1–890（890 aa） Chain AJ 1–890（890 aa） Chain AK 1–890（890 aa） Chain AL 1–890（890 aa） Chain AM 1–890（890 aa） Chain AN 1–890（890 aa） Chain AO 1–890（890 aa） Chain AP 1–890（890 aa） Chain B 1–890（890 aa） Chain C 1–890（890 aa） Chain D 1–890（890 aa） Chain E 1–890（890 aa） Chain F 1–890（890 aa） Chain G 1–890（890 aa） Chain H 1–890（890 aa） Chain I 1–890（890 aa） Chain J 1–890（890 aa） Chain K 1–890（890 aa） Chain L 1–890（890 aa） Chain M 1–890（890 aa） Chain N 1–890（890 aa） Chain O 1–890（890 aa） Chain P 1–890（890 aa） Chain Q 1–890（890 aa） Chain R 1–890（890 aa） Chain S 1–890（890 aa） Chain T 1–890（890 aa） Chain U 1–890（890 aa） Chain V 1–890（890 aa） Chain W 1–890（890 aa） Chain X 1–890（890 aa） Chain Y 1–890（890 aa） Chain Z 1–890（890 aa） Chain a 1–890（890 aa） Chain b 1–890（890 aa） Chain c 1–890（890 aa） Chain d 1–890（890 aa） Chain e 1–890（890 aa） Chain f 1–890（890 aa） Chain g 1–890（890 aa） Chain h 1–890（890 aa） Chain i 1–890（890 aa） Chain j 1–890（890 aa） Chain k 1–890（890 aa） Chain l 1–890（890 aa） Chain m 1–890（890 aa） Chain n 1–890（890 aa） Chain o 1–890（890 aa） Chain p 1–890（890 aa） Chain q 1–890（890 aa） Chain r 1–890（890 aa） Chain s 1–890（890 aa） Chain t 1–890（890 aa） Chain u 1–890（890 aa） Chain v 1–890（890 aa） Chain w 1–890（890 aa） Chain x 1–890（890 aa） Chain y 1–890（890 aa） Chain z 1–890（890 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.40 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	G1SVM1_RABIT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–140； UniProt 751–890 Author chain B； PDBConstruct 1–140； UniProt 751–890 Author chain C； PDBConstruct 1–140； UniProt 751–890 Author chain D； PDBConstruct 1–140； UniProt 751–890 Author chain E； PDBConstruct 1–140； UniProt 751–890 Author chain F； PDBConstruct 1–140； UniProt 751–890 Author chain G； PDBConstruct 1–140； UniProt 751–890 Author chain H； PDBConstruct 1–140； UniProt 751–890 Author chain I； PDBConstruct 1–140； UniProt 751–890 Author chain J； PDBConstruct 1–140； UniProt 751–890 Author chain K； PDBConstruct 1–140； UniProt 751–890 Author chain L； PDBConstruct 1–140； UniProt 751–890 Author chain M； PDBConstruct 1–140； UniProt 751–890 Author chain N； PDBConstruct 1–140； UniProt 751–890 Author chain O； PDBConstruct 1–140； UniProt 751–890 Author chain P； PDBConstruct 1–140； UniProt 751–890 Author chain Q； PDBConstruct 1–140； UniProt 751–890 Author chain R； PDBConstruct 1–140； UniProt 751–890 Author chain S； PDBConstruct 1–140； UniProt 751–890 Author chain T； PDBConstruct 1–140； UniProt 751–890 Author chain U； PDBConstruct 1–140； UniProt 751–890 Author chain V； PDBConstruct 1–140； UniProt 751–890 Author chain W； PDBConstruct 1–140； UniProt 751–890 Author chain X； PDBConstruct 1–140； UniProt 751–890 Author chain Y； PDBConstruct 1–140； UniProt 751–890 Author chain Z； PDBConstruct 1–140； UniProt 751–890 Author chain a； PDBConstruct 1–140； UniProt 751–890 Author chain b； PDBConstruct 1–140； UniProt 751–890 Author chain c； PDBConstruct 1–140； UniProt 751–890 Author chain d； PDBConstruct 1–140； UniProt 751–890 Author chain e； PDBConstruct 1–140； UniProt 751–890 Author chain f； PDBConstruct 1–140； UniProt 751–890 Author chain g； PDBConstruct 1–140； UniProt 751–890 Author chain h； PDBConstruct 1–140； UniProt 751–890 Author chain i； PDBConstruct 1–140； UniProt 751–890 Author chain j； PDBConstruct 1–140； UniProt 751–890 Author chain k； PDBConstruct 1–140； UniProt 751–890 Author chain l； PDBConstruct 1–140； UniProt 751–890 Author chain m； PDBConstruct 1–140； UniProt 751–890

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9z5n
Deposition date deposition_date	2025-11-12
Structure title title	Cryo-EM structure of rabbit vault cap
Keywords keywords	complex, MVP, vault cap, trafficking, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	70.75 Å
Radius of gyration Rg (electron density) rg_electron	70.14 Å
Forward intensity I(0) i0	2004640000.00
Molecular weight molecular_weight	394500.0 kDa
Excluded volume excluded_volume	502310 Å³
Envelope volume envelope_volume	1064300 Å³
Hydration-shell volume shell_volume	124690 Å³
Envelope diameter envelope_diameter	198.1 Å
Shell Rg shell_rg	72.96 Å
Envelope Rg envelope_rg	66.61 Å
Shape Rg shape_rg	70.13 Å
Total Rg total_rg	70.22 Å
Total atoms total_atoms	56719
Residues n_residues	3653
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

▼

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

Maximum dimension Dmax dmax	210.6 Å
Rg (real space) rg_real	70.63 Å
Rg uncertainty (real space) rg_real_error	1.47 Å
I(0) (real space) i0_real	2.0050e+09
I(0) uncertainty (real space) i0_real_error	4.0930e+07
Rg (reciprocal space) rg_reciprocal	70.91 Å
I(0) (reciprocal space) i0_reciprocal	2005000000.0000
Solution quality estimate total_estimate	0.8450
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	86.1 Å
Skewness Skewness skewness	0.075
Kurtosis Kurtosis kurtosis	-0.819
Angular range angular_range	— – 0.1100 Å⁻¹
Current regularization parameter α current_alpha	0.0007
Highest regularization parameter α highest_alpha	83940000.0000
Real-space data points n_real_points	23
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.998; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▶

8. Citations (1)

▶

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	—

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

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.25 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	129638

Description description	Major vault protein
Molecular weight formula_weight	14799.0 kDa
Source method src_method	nat
Copy count entity_count	39

Cryo-EM structure of rabbit vault cap

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

Major vault protein

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,a,b,c,d,e,f,g,h,i,j,k,l,m
Atom count atom_count	56719

fit	/app/data/saxs_computation/z5/9z5n/9z5n.fit
pddf	/app/data/pr_computation/z5/9z5n/9z5n.pr.out
profile	/app/data/saxs_computation/z5/9z5n/9z5n.dat