SAXSdb — 4abm

▼

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

CHARGED MULTIVESICULAR BODY PROTEIN 4B

HOMO SAPIENS

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 23–97 Chain B； UniProt 23–97	Fragment：CHMP4B HAIRPIN, RESIDUES 23-97	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.80 Å R-free 0.285
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 23–97	Fragment：CHMP4B HAIRPIN, RESIDUES 23-97	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.80 Å R-free 0.285
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 23–97	Fragment：CHMP4B HAIRPIN, RESIDUES 23-97	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.80 Å R-free 0.285

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 4ABM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3C3Q ALIX Bro1-domain:CHMIP4B co-crystal structure Deposited 2008-01-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 207–224（18 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；15% PEG 8,000, 100mM Na MES pH 6.5, 200mM Na Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.10 Å R-free 0.290
3UM3 Crystal structure of the Brox Bro1 domain in complex with the C-terminal tail of CHMP4B Deposited 2011-11-12	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 121–224（104 aa） Fragment：C-terminal tail of CHMP4B 121-224	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；273 K；1.0M sodium citrate, 0.1M imidazol, 15% glycerol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 3.80 Å R-free 0.243
5MK2 Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (CHMP4B peptide complex structure) Deposited 2016-12-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 205–224（20 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；0.2 M CaCl2, 0.1 M MES pH 6.0, 20% PEG 6K	Resolution 1.70 Å R-free 0.203

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CHM4B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–79； UniProt 23–97 Author chain B； PDBConstruct 5–79； UniProt 23–97 Author chain C； PDBConstruct 5–79； UniProt 23–97 Author chain D； PDBConstruct 5–79； UniProt 23–97

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	4abm
Deposition date deposition_date	2011-12-08
Structure title title	Crystal Structure of CHMP4B hairpin
Keywords keywords	CELL CYCLE, PROTEIN TRANSPORT, HIV-1; PROTEIN TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	23.50 Å
Radius of gyration Rg (electron density) rg_electron	22.68 Å
Forward intensity I(0) i0	24162300.00
Molecular weight molecular_weight	36648.0 kDa
Excluded volume excluded_volume	45907 Å³
Envelope volume envelope_volume	61050 Å³
Hydration-shell volume shell_volume	23225 Å³
Envelope diameter envelope_diameter	91.5 Å
Shell Rg shell_rg	28.92 Å
Envelope Rg envelope_rg	23.18 Å
Shape Rg shape_rg	22.64 Å
Total Rg total_rg	23.64 Å
Total atoms total_atoms	2568
Residues n_residues	313
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	89.0 Å
Rg (real space) rg_real	23.49 Å
Rg uncertainty (real space) rg_real_error	0.86 Å
I(0) (real space) i0_real	2.4160e+07
I(0) uncertainty (real space) i0_real_error	3.4300e+05
Rg (reciprocal space) rg_reciprocal	23.49 Å
I(0) (reciprocal space) i0_reciprocal	24160000.0000
Solution quality estimate total_estimate	0.8184
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.1 Å
Skewness Skewness skewness	0.392
Kurtosis Kurtosis kurtosis	0.097
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2915000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.572; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.922; Smooth: 0.998

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4abmA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1060 — ESAT-6-like

Domain ID domain_id	4abmB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1060 — ESAT-6-like

Domain ID domain_id	4abmC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1060 — ESAT-6-like

Domain ID domain_id	4abmD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1060 — ESAT-6-like

▶

8. Citations (1)

▶

Unit-cell length a length_a	37.590 Å
Unit-cell length b length_b	71.430 Å
Unit-cell length c length_c	123.680 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	61.860 Å
R factor r_factor	0.2304
R_work r_work	0.2276
R_free r_free	0.2852

Description description	CHARGED MULTIVESICULAR BODY PROTEIN 4B
Molecular weight formula_weight	9249.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	2830

Crystal Structure of CHMP4B hairpin

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

CHARGED MULTIVESICULAR BODY PROTEIN 4B

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 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	137

fit	/app/data/saxs_computation/ab/4abm/4abm.fit
pddf	/app/data/pr_computation/ab/4abm/4abm.pr.out
profile	/app/data/saxs_computation/ab/4abm/4abm.dat