9e9v

Structural Insights into HIV-1 Vif-Mediated Ubiquitination and Degradation of APOBEC3H

Method: ELECTRON MICROSCOPY

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

single-stranded DNA cytosine deaminase

Pan troglodytes

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 9 RNA 4	;RNA (5'-R(PCPCPCPGPGPCPA)-3') ; × 2 ;RNA (5'-R(PGPCPCPGPGP*G)-3') ; × 2 Elongin-C × 1 （Q15369） Elongin-B × 1 （Q15370） Virion infectivity factor × 2 （P12504） Core-binding factor subunit beta × 2 （Q13951） ZINC ION × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

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

Elongin-C

Homo sapiens

UniProt Q15369

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 9 RNA 4	single-stranded DNA cytosine deaminase × 3 （B7T0U6） ;RNA (5'-R(PCPCPCPGPGPCPA)-3') ; × 2 ;RNA (5'-R(PGPCPCPGPGP*G)-3') ; × 2 Elongin-B × 1 （Q15370） Virion infectivity factor × 2 （P12504） Core-binding factor subunit beta × 2 （Q13951） ZINC ION × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ELOC_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain n； PDBConstruct 1–96； UniProt 17–112

Elongin-B

Homo sapiens

UniProt Q15370

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 9 RNA 4	single-stranded DNA cytosine deaminase × 3 （B7T0U6） ;RNA (5'-R(PCPCPCPGPGPCPA)-3') ; × 2 ;RNA (5'-R(PGPCPCPGPGP*G)-3') ; × 2 Elongin-C × 1 （Q15369） Virion infectivity factor × 2 （P12504） Core-binding factor subunit beta × 2 （Q13951） ZINC ION × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ELOB_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain m； PDBConstruct 1–102； UniProt 1–102

Virion infectivity factor

Human immunodeficiency virus 1

UniProt P12504

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 9 RNA 4	single-stranded DNA cytosine deaminase × 3 （B7T0U6） ;RNA (5'-R(PCPCPCPGPGPCPA)-3') ; × 2 ;RNA (5'-R(PGPCPCPGPGP*G)-3') ; × 2 Elongin-C × 1 （Q15369） Elongin-B × 1 （Q15370） Core-binding factor subunit beta × 2 （Q13951） ZINC ION × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VIF_HV1N5
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain p； PDBConstruct 1–176； UniProt 1–176 Author chain t； PDBConstruct 1–176； UniProt 1–176

Core-binding factor subunit beta

Homo sapiens

UniProt Q13951

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 9 RNA 4	single-stranded DNA cytosine deaminase × 3 （B7T0U6） ;RNA (5'-R(PCPCPCPGPGPCPA)-3') ; × 2 ;RNA (5'-R(PGPCPCPGPGP*G)-3') ; × 2 Elongin-C × 1 （Q15369） Elongin-B × 1 （Q15370） Virion infectivity factor × 2 （P12504） ZINC ION × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PEBB_HUMAN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain o； PDBConstruct 1–170； UniProt 1–170 Author chain s； PDBConstruct 1–170； UniProt 1–170

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	9e9v
Deposition date deposition_date	2024-11-08
Structure title title	Structural Insights into HIV-1 Vif-Mediated Ubiquitination and Degradation of APOBEC3H
Keywords keywords	APOBEC3H HIV-1 Vif, VIRAL PROTEIN, VIRAL PROTEIN-RNA complex; VIRAL PROTEIN/RNA
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9e9v__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9e9v__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9e9v__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	39.23 Å
Rg (electron density)	38.52 Å
Total Rg	38.97 Å
Atom count	10935
Residues	1273
Excluded volume	191650 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9e9v__assembly_1__model_1`	13-meric （13）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	single-stranded DNA cytosine deaminase
Molecular weight formula_weight	21768.2 kDa
EC 编号 ec_number	3.5.4.38
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,E
Atom count atom_count	10935

MALLTAETFRLQFNNRRRLRRPYYPRKALLCYQLTPQNGSTPTRGYFENKKKCHAEICFINEIKSMGLDETQCYQVTCYLTWSPCSSCAWKLVDFIQAHDHLNLRIFASRLYYHWCKPQQEGLRLLCGSQVPVEVMGLPEFNDCWENFVDHEKPLSFDPCKMLEELDKNSRAIKRRLERIKQS

Source Source

Source organism organism	Pan troglodytes
Common name common_name	chimpanzee
NCBI taxonomy ID ncbi_taxonomy_id	9598
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	;RNA (5'-R(PCPCPCPGPGPCP*A)-3') ;
Molecular weight formula_weight	3160.0 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	D,H

AUACCCGGCA

Entity 3 Entity 3 polymer

Description description	;RNA (5'-R(PGPCPCPGPGPG)-3') ;
Molecular weight formula_weight	2887.8 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C,G

UGCCGGGUA

Entity 4 Entity 4 polymer

Description description	Elongin-C
Molecular weight formula_weight	10843.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	n

MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	Elongin-B
Molecular weight formula_weight	11488.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	m

MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDV

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 6 Entity 6 polymer

Description description	Virion infectivity factor
Molecular weight formula_weight	20982.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	p,t

MENRWQVMIVWQVDRMRINTWKRLVKHHMYISRKAKDWFYRHHYESTNPKISSEVHIPLGDAKLVITTYWGLHTGERDWHLGQGVSIEWRKKRYSTQVDPDLADQLIHLHYFDCFSESAIRNTILGRIVSPRCEYQAGHNKVGSLQYLALAALIKPKQIKPPLPSVRKLTEDRWNK

Source Source

Source organism organism	Human immunodeficiency virus 1
NCBI taxonomy ID ncbi_taxonomy_id	11676
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 7 Entity 7 polymer

Description description	Core-binding factor subunit beta
Molecular weight formula_weight	20272.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	o,s

MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVATGTNLSLQFFPASWQGEQRQTPSREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLQRLDGMGCLEFDEERAQQEDALAQQAFEEARRRTREFEDRDRSHREEMEVRVSQ

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 8 Entity 8 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

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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	4.00 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	215818

Structural Insights into HIV-1 Vif-Mediated Ubiquitination and Degradation of APOBEC3H

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

single-stranded DNA cytosine deaminase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Elongin-C

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Elongin-B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Virion infectivity factor

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Core-binding factor subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9e9v__assembly_1__model_1

9e9v__assembly_1__model_1 | I(q)

9e9v__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

Entity 8 Entity 8 non-polymer

7. Citations (1)