8fvi

Human APOBEC3H bound to HIV-1 Vif in complex with CBF-beta, ELOB, ELOC, and CUL5

Method: ELECTRON MICROSCOPY

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

Core-binding factor subunit beta

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 6 RNA 2	Virion infectivity factor × 1 （P12504） DNA dC->dU-editing enzyme APOBEC-3H × 1 （Q6NTF7） RNA(5'-R(APUPUPUPUPUPUPUPUPU)-3') × 1 RNA(5'-R(APAPAPAPAPAPAPAPA)-3') × 1 Cullin 5 × 1 （A0A2K5ZN28） Elongin-B × 1 （Q15370） Elongin-C × 1 （Q15369） ZINC ION × 2 water × 1	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	1
Chains and sequence ranges	Author chain 0； PDBConstruct 1–157； UniProt 1–157

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 6 RNA 2	Core-binding factor subunit beta × 1 （Q13951） DNA dC->dU-editing enzyme APOBEC-3H × 1 （Q6NTF7） RNA(5'-R(APUPUPUPUPUPUPUPUPU)-3') × 1 RNA(5'-R(APAPAPAPAPAPAPAPA)-3') × 1 Cullin 5 × 1 （A0A2K5ZN28） Elongin-B × 1 （Q15370） Elongin-C × 1 （Q15369） ZINC ION × 2 water × 1	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	2
Chains and sequence ranges	Author chain 1； PDBConstruct 3–178； UniProt 1–176

DNA dC->dU-editing enzyme APOBEC-3H

Homo sapiens

UniProt Q6NTF7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 6 RNA 2	Core-binding factor subunit beta × 1 （Q13951） Virion infectivity factor × 1 （P12504） RNA(5'-R(APUPUPUPUPUPUPUPUPU)-3') × 1 RNA(5'-R(APAPAPAPAPAPAPAPA)-3') × 1 Cullin 5 × 1 （A0A2K5ZN28） Elongin-B × 1 （Q15370） Elongin-C × 1 （Q15369） ZINC ION × 2 water × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ABC3H_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 8–188； UniProt 1–181

Cullin 5

Homo sapiens

UniProt A0A2K5ZN28

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 6 RNA 2	Core-binding factor subunit beta × 1 （Q13951） Virion infectivity factor × 1 （P12504） DNA dC->dU-editing enzyme APOBEC-3H × 1 （Q6NTF7） RNA(5'-R(APUPUPUPUPUPUPUPUPU)-3') × 1 RNA(5'-R(APAPAPAPAPAPAPAPA)-3') × 1 Elongin-B × 1 （Q15370） Elongin-C × 1 （Q15369） ZINC ION × 2 water × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A2K5ZN28_MANLE
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain x； PDBConstruct 5–314； UniProt 9–318

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 6 RNA 2	Core-binding factor subunit beta × 1 （Q13951） Virion infectivity factor × 1 （P12504） DNA dC->dU-editing enzyme APOBEC-3H × 1 （Q6NTF7） RNA(5'-R(APUPUPUPUPUPUPUPUPU)-3') × 1 RNA(5'-R(APAPAPAPAPAPAPAPA)-3') × 1 Cullin 5 × 1 （A0A2K5ZN28） Elongin-C × 1 （Q15369） ZINC ION × 2 water × 1	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	7
Chains and sequence ranges	Author chain y； PDBConstruct 1–102； UniProt 1–102

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 6 RNA 2	Core-binding factor subunit beta × 1 （Q13951） Virion infectivity factor × 1 （P12504） DNA dC->dU-editing enzyme APOBEC-3H × 1 （Q6NTF7） RNA(5'-R(APUPUPUPUPUPUPUPUPU)-3') × 1 RNA(5'-R(APAPAPAPAPAPAPAPA)-3') × 1 Cullin 5 × 1 （A0A2K5ZN28） Elongin-B × 1 （Q15370） ZINC ION × 2 water × 1	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	8
Chains and sequence ranges	Author chain z； PDBConstruct 1–96； UniProt 17–112

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	8fvi
Deposition date deposition_date	2023-01-19
Structure title title	Human APOBEC3H bound to HIV-1 Vif in complex with CBF-beta, ELOB, ELOC, and CUL5
Keywords keywords	virus-host protein complex, ANTIVIRAL PROTEIN; ANTIVIRAL PROTEIN
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.

8fvi__assembly_1__model_1

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

Download this curve (.dat)

8fvi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8fvi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.78 Å
Rg (electron density)	36.08 Å
Total Rg	36.44 Å
Atom count	6773
Residues	796
Excluded volume	119310 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8fvi__assembly_1__model_1`	octameric （8）	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 (10)

Entity 1 Entity 1 polymer

Description description	Core-binding factor subunit beta
Molecular weight formula_weight	18643.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	0
Atom count atom_count	6774

MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVATGTNLSLQFFPASWQGEQRQTPSREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLQRLDGMGCLEFDEERAQQEDALAQQAFEEARRRTREFEDRD

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

Entity 2 Entity 2 polymer

Description description	Virion infectivity factor
Molecular weight formula_weight	21160.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1

GPMENRWQVMIVWQVDRMRINTWKRLVKHHMYISRKAKDWFYRHHYESTHPKISSEVHIPLGDAKLVITTYWGLHTGERDWHLGQGVSIEWRKKRYSTQVDPDLADQLIHLHYFDCFSESAIRNTILGRIVSPRCEYQAGHNKVGSLQYLALAALIKPKQIKPPLPSVRKLTEDRWNK

Source Source

Source organism organism	Human immunodeficiency virus 1
NCBI taxonomy ID ncbi_taxonomy_id	11676
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	DNA dC->dU-editing enzyme APOBEC-3H
Molecular weight formula_weight	22103.4 kDa
EC 编号 ec_number	3.5.4.38
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

GPGGSGGMALLTAETFRLQFNNKRRLRRPYYPRKALLCYQLTPQNGSTPTRGYFENKKKCHAEICFINEIKSMGLDETQCYQVTCYLTWSPCSSCAWELVDFIQAHDHLNLRIFASRLYYHWCKPQQDGLRLLCGSQVPVEVMGFPEFADCWENFVDHEKPLSFNPYKMLEELDKNSRAIKRRLDRIKS

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

Entity 4 Entity 4 polymer

Description description	RNA(5'-R(APUPUPUPUPUPUPUPUP*U)-3')
Molecular weight formula_weight	3039.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B

AUUUUUUUUU

Entity 5 Entity 5 polymer

Description description	RNA(5'-R(APAPAPAPAPAPAPAP*A)-3')
Molecular weight formula_weight	2917.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C

AAAAAAAAA

Entity 6 Entity 6 polymer

Description description	Cullin 5
Molecular weight formula_weight	36614.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	x

GPAGSSLQFEDKWDFMRPIVLKLLRQESVTKQQWFDLFSDVHAVCLWDDKGPAKIHQALKEDILEFIKQAQARVLSHQDDTALLKAYIVEWRKFFTQCDILPKPFCQLEITLMGKQGSNKKSNVEDSIVRKLMLDTWNESIFSNIKNRLQDSAMKLVHAERLGEAFDSQLVIGVRESYVNLCSNPEDKLQIYRDNFEKAYLDSTERFYRTQAPSYLQQNGVQNYMKYADAKLKEEEKRALRYLETRRECNSVEALMECCVNALVTSFKETILAECQGMIKRNETEKLHLMFSLMDKVPNGIEPMLKDLEEHIIS

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

Entity 7 Entity 7 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	y

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

Entity 8 Entity 8 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	z

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

Entity 9 Entity 9 non-polymer

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

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	8fvix01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1310 — 5 helical Cullin repeat like
Homologous superfamily homologous superfamily	10 — Cullin Repeats

Domain ID domain_id	8fviz01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily	10 — Potassium Channel Kv1.1; Chain A

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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	3.24 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	89986

Human APOBEC3H bound to HIV-1 Vif in complex with CBF-beta, ELOB, ELOC, and CUL5

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

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

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

DNA dC->dU-editing enzyme APOBEC-3H

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cullin 5

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8fvi__assembly_1__model_1

8fvi__assembly_1__model_1 | I(q)

8fvi__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

Entity 8 Entity 8 polymer