SAXSdb — 5z98

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

Apolipoprotein B mRNA editing enzyme catalytic polypeptide-like protein 3H

Pan troglodytes

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–RNA Homooligomer Protein × 2 RNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 1–183 Chain B； UniProt 1–183	Not recorded	;RNA (5'-R(PCPUPGPCPCPGPGPGPUPA)-3') ; × 1 ;RNA (5'-R(APUPAPCPCPCPGPGPCPA)-3') ; × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；10% PEG 3350, 100mM ammonium formate	Resolution 2.20 Å R-free 0.320

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 5Z98	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9E93 Structural Insights into HIV-1 Vif-Mediated Ubiquitination and Degradation of APOBEC3H Deposited 2024-11-07	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: decameric	Chain A 1–183（183 aa） Chain E 1–183（183 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.58 Å
9E9V Structural Insights into HIV-1 Vif-Mediated Ubiquitination and Degradation of APOBEC3H Deposited 2024-11-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 9 PDB declaration: 13-meric	Chain A 1–183（183 aa） Chain B 1–183（183 aa） Chain E 1–183（183 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	B7T0U6_PANTR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–185； UniProt 1–183 Author chain B； PDBConstruct 3–185； UniProt 1–183

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	5z98
Deposition date deposition_date	2018-02-02
Structure title title	Crystal Structure of the Primate APOBEC3H Dimer mediated by RNA Duplex
Keywords keywords	;APOBEC3, APOBEC3H, cytidine deaminase, deaminase, anti-HIV, Vif, dsRNA, cancer, HIV-1, SIV, chimpanzee, dimerization, Pan troglodytes, ANTIVIRAL PROTEIN-RNA complex ;; ANTIVIRAL PROTEIN/RNA
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	28.06 Å
Radius of gyration Rg (electron density) rg_electron	26.80 Å
Forward intensity I(0) i0	48115100.00
Molecular weight molecular_weight	48956.0 kDa
Excluded volume excluded_volume	59113 Å³
Envelope volume envelope_volume	77085 Å³
Hydration-shell volume shell_volume	24822 Å³
Envelope diameter envelope_diameter	90.6 Å
Shell Rg shell_rg	32.89 Å
Envelope Rg envelope_rg	26.61 Å
Shape Rg shape_rg	26.71 Å
Total Rg total_rg	27.66 Å
Total atoms total_atoms	3400
Residues n_residues	384
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	89.2 Å
Rg (real space) rg_real	28.19 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	4.8120e+07
I(0) uncertainty (real space) i0_real_error	7.2230e+05
Rg (reciprocal space) rg_reciprocal	28.15 Å
I(0) (reciprocal space) i0_reciprocal	48110000.0000
Solution quality estimate total_estimate	0.8833
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	25.0 Å
Skewness Skewness skewness	0.352
Kurtosis Kurtosis kurtosis	-0.637
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10230000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.886; Smooth: 0.844

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Apolipoprotein B mRNA editing enzyme catalytic polypeptide-like protein 3H
Molecular weight formula_weight	21912.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3477

GSMALLTAETFRLQFNNRRRLRRPYYPRKALLCYQLTPQNGSTPTRGYFENKKKCHAEICFINEIKSMGLDETQCYQVTCYLTWSPCSSCAWKLVDFIQAHDHLNLRIFASRLYYHWCKPQQEGLRLLCGSQVPVEVMGLPEFNDCWENFVDHEKPLSFDPCKMLEELDKNSRAIKRRLERIKQS

来源 Source

来源生物 organism	Pan troglodytes
通用名 common_name	Chimpanzee
NCBI Class编号 ncbi_taxonomy_id	9598
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;RNA (5'-R(PCPUPGPCPCPGPGPGPUPA)-3') ;
Molecular weight formula_weight	3192.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C

CUGCCGGGUA

来源 Source

来源生物 organism	unidentified
NCBI Class编号 ncbi_taxonomy_id	32644
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	;RNA (5'-R(APUPAPCPCPCPGPGPCPA)-3') ;
Molecular weight formula_weight	3160.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	D

AUACCCGGCA

来源 Source

来源生物 organism	unidentified
NCBI Class编号 ncbi_taxonomy_id	32644
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	77

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8. Citations (1)

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Unit-cell length a length_a	38.341 Å
Unit-cell length b length_b	86.970 Å
Unit-cell length c length_c	77.363 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.63 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	43.485 Å
R factor r_factor	0.2545
R_work r_work	0.2511
R_free r_free	0.3202

fit	/app/data/saxs_computation/z9/5z98/5z98.fit
pddf	/app/data/pr_computation/z9/5z98/5z98.pr.out
profile	/app/data/saxs_computation/z9/5z98/5z98.dat

Crystal Structure of the Primate APOBEC3H Dimer mediated by RNA Duplex

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

Apolipoprotein B mRNA editing enzyme catalytic polypeptide-like protein 3H

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)