SAXSdb — 9z4w

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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 × 78 PDB declaration: 78-meric（78） Consistent with protein copy count	Chain 0； UniProt 1–890 Chain 1； UniProt 1–890 Chain 2； UniProt 1–890 Chain 3； UniProt 1–890 Chain 4； UniProt 1–890 Chain 5； UniProt 1–890 Chain 6； UniProt 1–890 Chain 7； UniProt 1–890 Chain 8； UniProt 1–890 Chain 9； UniProt 1–890 Chain A； UniProt 1–890 Chain AA； UniProt 1–890 Chain AB； UniProt 1–890 Chain AC； UniProt 1–890 Chain AD； UniProt 1–890 Chain AE； UniProt 1–890 Chain AF； UniProt 1–890 Chain AG； UniProt 1–890 Chain AH； UniProt 1–890 Chain AI； UniProt 1–890 Chain AJ； UniProt 1–890 Chain AK； UniProt 1–890 Chain AL； UniProt 1–890 Chain AM； UniProt 1–890 Chain AN； UniProt 1–890 Chain AO； UniProt 1–890 Chain AP； UniProt 1–890 Chain B； UniProt 1–890 Chain C； UniProt 1–890 Chain D； UniProt 1–890 Chain E； UniProt 1–890 Chain F； UniProt 1–890 Chain G； UniProt 1–890 Chain H； UniProt 1–890 Chain I； UniProt 1–890 Chain J； UniProt 1–890 Chain K； UniProt 1–890 Chain L； UniProt 1–890 Chain M； UniProt 1–890 Chain N； UniProt 1–890 Chain O； UniProt 1–890 Chain P； UniProt 1–890 Chain Q； UniProt 1–890 Chain R； UniProt 1–890 Chain S； UniProt 1–890 Chain T； UniProt 1–890 Chain U； UniProt 1–890 Chain V； UniProt 1–890 Chain W； UniProt 1–890 Chain X； UniProt 1–890 Chain Y； UniProt 1–890 Chain Z； UniProt 1–890 Chain a； UniProt 1–890 Chain b； UniProt 1–890 Chain c； UniProt 1–890 Chain d； UniProt 1–890 Chain e； UniProt 1–890 Chain f； UniProt 1–890 Chain g； UniProt 1–890 Chain h； UniProt 1–890 Chain i； UniProt 1–890 Chain j； UniProt 1–890 Chain k； UniProt 1–890 Chain l； UniProt 1–890 Chain m； UniProt 1–890 Chain n； UniProt 1–890 Chain o； UniProt 1–890 Chain p； UniProt 1–890 Chain q； UniProt 1–890 Chain r； UniProt 1–890 Chain s； UniProt 1–890 Chain t； UniProt 1–890 Chain u； UniProt 1–890 Chain v； UniProt 1–890 Chain w； UniProt 1–890 Chain x； UniProt 1–890 Chain y； UniProt 1–890 Chain z； UniProt 1–890	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 6.8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.40 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 9Z4W	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9Z5N Cryo-EM structure of rabbit vault cap Deposited 2025-11-12	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 39 PDB declaration: 39-meric	Chain A 751–890（140 aa） Chain B 751–890（140 aa） Chain C 751–890（140 aa） Chain D 751–890（140 aa） Chain E 751–890（140 aa） Chain F 751–890（140 aa） Chain G 751–890（140 aa） Chain H 751–890（140 aa） Chain I 751–890（140 aa） Chain J 751–890（140 aa） Chain K 751–890（140 aa） Chain L 751–890（140 aa） Chain M 751–890（140 aa） Chain N 751–890（140 aa） Chain O 751–890（140 aa） Chain P 751–890（140 aa） Chain Q 751–890（140 aa） Chain R 751–890（140 aa） Chain S 751–890（140 aa） Chain T 751–890（140 aa） Chain U 751–890（140 aa） Chain V 751–890（140 aa） Chain W 751–890（140 aa） Chain X 751–890（140 aa） Chain Y 751–890（140 aa） Chain Z 751–890（140 aa） Chain a 751–890（140 aa） Chain b 751–890（140 aa） Chain c 751–890（140 aa） Chain d 751–890（140 aa） Chain e 751–890（140 aa） Chain f 751–890（140 aa） Chain g 751–890（140 aa） Chain h 751–890（140 aa） Chain i 751–890（140 aa） Chain j 751–890（140 aa） Chain k 751–890（140 aa） Chain l 751–890（140 aa） Chain m 751–890（140 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.25 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 0； PDBConstruct 1–890； UniProt 1–890 Author chain 1； PDBConstruct 1–890； UniProt 1–890 Author chain 2； PDBConstruct 1–890； UniProt 1–890 Author chain 3； PDBConstruct 1–890； UniProt 1–890 Author chain 4； PDBConstruct 1–890； UniProt 1–890 Author chain 5； PDBConstruct 1–890； UniProt 1–890 Author chain 6； PDBConstruct 1–890； UniProt 1–890 Author chain 7； PDBConstruct 1–890； UniProt 1–890 Author chain 8； PDBConstruct 1–890； UniProt 1–890 Author chain 9； PDBConstruct 1–890； UniProt 1–890 Author chain A； PDBConstruct 1–890； UniProt 1–890 Author chain AA； PDBConstruct 1–890； UniProt 1–890 Author chain AB； PDBConstruct 1–890； UniProt 1–890 Author chain AC； PDBConstruct 1–890； UniProt 1–890 Author chain AD； PDBConstruct 1–890； UniProt 1–890 Author chain AE； PDBConstruct 1–890； UniProt 1–890 Author chain AF； PDBConstruct 1–890； UniProt 1–890 Author chain AG； PDBConstruct 1–890； UniProt 1–890 Author chain AH； PDBConstruct 1–890； UniProt 1–890 Author chain AI； PDBConstruct 1–890； UniProt 1–890 Author chain AJ； PDBConstruct 1–890； UniProt 1–890 Author chain AK； PDBConstruct 1–890； UniProt 1–890 Author chain AL； PDBConstruct 1–890； UniProt 1–890 Author chain AM； PDBConstruct 1–890； UniProt 1–890 Author chain AN； PDBConstruct 1–890； UniProt 1–890 Author chain AO； PDBConstruct 1–890； UniProt 1–890 Author chain AP； PDBConstruct 1–890； UniProt 1–890 Author chain B； PDBConstruct 1–890； UniProt 1–890 Author chain C； PDBConstruct 1–890； UniProt 1–890 Author chain D； PDBConstruct 1–890； UniProt 1–890 Author chain E； PDBConstruct 1–890； UniProt 1–890 Author chain F； PDBConstruct 1–890； UniProt 1–890 Author chain G； PDBConstruct 1–890； UniProt 1–890 Author chain H； PDBConstruct 1–890； UniProt 1–890 Author chain I； PDBConstruct 1–890； UniProt 1–890 Author chain J； PDBConstruct 1–890； UniProt 1–890 Author chain K； PDBConstruct 1–890； UniProt 1–890 Author chain L； PDBConstruct 1–890； UniProt 1–890 Author chain M； PDBConstruct 1–890； UniProt 1–890 Author chain N； PDBConstruct 1–890； UniProt 1–890 Author chain O； PDBConstruct 1–890； UniProt 1–890 Author chain P； PDBConstruct 1–890； UniProt 1–890 Author chain Q； PDBConstruct 1–890； UniProt 1–890 Author chain R； PDBConstruct 1–890； UniProt 1–890 Author chain S； PDBConstruct 1–890； UniProt 1–890 Author chain T； PDBConstruct 1–890； UniProt 1–890 Author chain U； PDBConstruct 1–890； UniProt 1–890 Author chain V； PDBConstruct 1–890； UniProt 1–890 Author chain W； PDBConstruct 1–890； UniProt 1–890 Author chain X； PDBConstruct 1–890； UniProt 1–890 Author chain Y； PDBConstruct 1–890； UniProt 1–890 Author chain Z； PDBConstruct 1–890； UniProt 1–890 Author chain a； PDBConstruct 1–890； UniProt 1–890 Author chain b； PDBConstruct 1–890； UniProt 1–890 Author chain c； PDBConstruct 1–890； UniProt 1–890 Author chain d； PDBConstruct 1–890； UniProt 1–890 Author chain e； PDBConstruct 1–890； UniProt 1–890 Author chain f； PDBConstruct 1–890； UniProt 1–890 Author chain g； PDBConstruct 1–890； UniProt 1–890 Author chain h； PDBConstruct 1–890； UniProt 1–890 Author chain i； PDBConstruct 1–890； UniProt 1–890 Author chain j； PDBConstruct 1–890； UniProt 1–890 Author chain k； PDBConstruct 1–890； UniProt 1–890 Author chain l； PDBConstruct 1–890； UniProt 1–890 Author chain m； PDBConstruct 1–890； UniProt 1–890 Author chain n； PDBConstruct 1–890； UniProt 1–890 Author chain o； PDBConstruct 1–890； UniProt 1–890 Author chain p； PDBConstruct 1–890； UniProt 1–890 Author chain q； PDBConstruct 1–890； UniProt 1–890 Author chain r； PDBConstruct 1–890； UniProt 1–890 Author chain s； PDBConstruct 1–890； UniProt 1–890 Author chain t； PDBConstruct 1–890； UniProt 1–890 Author chain u； PDBConstruct 1–890； UniProt 1–890 Author chain v； PDBConstruct 1–890； UniProt 1–890 Author chain w； PDBConstruct 1–890； UniProt 1–890 Author chain x； PDBConstruct 1–890； UniProt 1–890 Author chain y； PDBConstruct 1–890； UniProt 1–890 Author chain z； PDBConstruct 1–890； UniProt 1–890

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9z4w
Deposition date deposition_date	2025-11-11
Structure title title	Cryo-EM structure of rabbit major vault protein complex
Keywords keywords	complex, MVP, vault cap, trafficking, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
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	— Å
Radius of gyration Rg (electron density) rg_electron	227.60 Å
Forward intensity I(0) i0	653661000000.00
Molecular weight molecular_weight	6969500.0 kDa
Excluded volume excluded_volume	8747300 Å³
Envelope volume envelope_volume	47530000 Å³
Hydration-shell volume shell_volume	1882000 Å³
Envelope diameter envelope_diameter	673.6 Å
Shell Rg shell_rg	224.40 Å
Envelope Rg envelope_rg	186.90 Å
Shape Rg shape_rg	227.50 Å
Total Rg total_rg	228.00 Å
Total atoms total_atoms	491504
Residues n_residues	62530
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	632.4 Å
Rg (real space) rg_real	227.70 Å
Rg uncertainty (real space) rg_real_error	2.49 Å
I(0) (real space) i0_real	6.4160e+11
I(0) uncertainty (real space) i0_real_error	1.7730e+10
Rg (reciprocal space) rg_reciprocal	171.60 Å
I(0) (reciprocal space) i0_reciprocal	361100000000.0000
Solution quality estimate total_estimate	0.8843
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	361.4 Å
Skewness Skewness skewness	-0.063
Kurtosis Kurtosis kurtosis	-0.552
Angular range angular_range	— – 0.0350 Å⁻¹
Current regularization parameter α current_alpha	2.2800
Highest regularization parameter α highest_alpha	31860000000.0000
Real-space data points n_real_points	8
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 9.160; Oscil: 0.973; Stabil: 0.910; Sysdev: 1.000; Positv: 1.000; Valcen: 0.861; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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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	—

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

Resolution resolution	2.40 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	159668

Description description	Major vault protein
Molecular weight formula_weight	98695.2 kDa
Source method src_method	nat
Copy count entity_count	78

Polymer type type	polypeptide(L)
Chain IDs strand_id	;A,B,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,n,o,p,q,r,s,t,u,v,w,x,y,z,0,1,2,3,4,5,6,7,8,9,AA,AB,AC,AD,AE,AF,AG,AH,AI,AJ,AK,AL,AM,AN,AO,AP ;
Atom count atom_count	491504

Cryo-EM structure of rabbit major vault protein complex

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

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)

fit	/app/data/saxs_computation/z4/9z4w/9z4w.fit
pddf	/app/data/pr_computation/z4/9z4w/9z4w.pr.out
profile	/app/data/saxs_computation/z4/9z4w/9z4w.dat