SAXSdb — 4z8l

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

Protein VPRBP

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Vpx protein × 1 （Q7ZB17） SAM domain and HD domain-containing protein × 1 （H6WEA4） ZINC ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Vpx protein × 1 （Q7ZB17） SAM domain and HD domain-containing protein × 1 （H6WEA4） ZINC ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VPRBP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–341； UniProt 1057–1396 Author chain D； PDBConstruct 2–341； UniProt 1057–1396

Vpx protein

Simian immunodeficiency virus

UniProt Q7ZB17

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Protein VPRBP × 1 （Q9Y4B6） SAM domain and HD domain-containing protein × 1 （H6WEA4） ZINC ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Protein VPRBP × 1 （Q9Y4B6） SAM domain and HD domain-containing protein × 1 （H6WEA4） ZINC ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7ZB17_SIV
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–92； UniProt 1–89 Author chain E； PDBConstruct 4–92； UniProt 1–89

SAM domain and HD domain-containing protein

Mandrillus sphinx

UniProt H6WEA4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Protein VPRBP × 1 （Q9Y4B6） Vpx protein × 1 （Q7ZB17） ZINC ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Protein VPRBP × 1 （Q9Y4B6） Vpx protein × 1 （Q7ZB17） ZINC ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H6WEA4_MANSP
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 4–118； UniProt 1–115 Author chain F； PDBConstruct 4–118； UniProt 1–115

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	4z8l
Deposition date deposition_date	2015-04-09
Structure title title	Crystal structure of DCAF1/SIV-MND VPX/MND SAMHD1 NTD ternary complex
Keywords keywords	HIV, antiviral defense, Viral Protein-VPX-BINDING PROTEIN complex; Viral Protein/VPX-BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

4z8l__assembly_1__model_1

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

Download this curve (.dat)

4z8l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4z8l__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.42 Å
Rg (electron density)	24.99 Å
Total Rg	25.64 Å
Atom count	3847
Residues	476
Excluded volume	67804 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4z8l__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4z8l__assembly_2__model_1`	trimeric （3）	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 (5)

Entity 1 Entity 1 polymer

Description description	Protein VPRBP
Molecular weight formula_weight	39777.7 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	7828

ARASFPKYGGVDGGCFDRHLIFSRFRPISVFREANEDESGFTCCAFSARERFLMLGTCTGQLKLYNVFSGQEEASYNCHNSAITHLEPSRDGSLLLTSATWSQPLSALWGMKSVFDMKHSFTEDHYVEFSKHSQDRVIGTKGDIAHIYDIQTGNKLLTLFNPDLANNYKRNCATFNPTDDLVLNDGVLWDVRSAQAIHKFDKFNMNISGVFHPNGLEVIINTEIWDLRTFHLLHTVPALDQCRVVFNHTGTVMYGAMLQADDEDDLMEERMKSPFGSSFRTFNATDYKPIATIDVKRNIFDLCTDTKDCYLAVIENQGSMDALNMDTVCRLYEVGRQRLAELEHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Baculoviridae

Entity 2 Entity 2 polymer

Description description	Vpx protein
Molecular weight formula_weight	12204.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

SEFMAERAPEAPEGAGEVGLEQWLETSLERINREARLHFHPEFLFRLWNTCVEHWHDRHQRSLDYAKYRYLLLMHKAMYTHMQQGCPCRNGRLEHHHHHH

Source Source

Source organism organism	Simian immunodeficiency virus
Common name common_name	SIV
NCBI taxonomy ID ncbi_taxonomy_id	11723
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	SAM domain and HD domain-containing protein
Molecular weight formula_weight	13197.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

SEFMQQADSDQPSKRPRFDDSPRTPSSTPSAEADCSPGVELHPDYKTWGPEQVCFFLRRGGFGEPALLKNIRENKITGALLPCLDESHFENLGVSSLGERKKLLSYIQRSGQIHVDTM

Source Source

Source organism organism	Mandrillus sphinx
Common name common_name	Mandrill
NCBI taxonomy ID ncbi_taxonomy_id	9561
Host organism 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	114

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4z8lA00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	4z8lB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	4730 —

Domain ID domain_id	4z8lD00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	4z8lE00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	4730 —

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Unit-cell length a length_a	74.490 Å
Unit-cell length b length_b	74.490 Å
Unit-cell length c length_c	178.180 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	43.695 Å
R factor r_factor	0.2015
R_work r_work	0.1992
R_free r_free	0.2277

Crystal structure of DCAF1/SIV-MND VPX/MND SAMHD1 NTD ternary complex

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

Protein VPRBP

State in the Current Structure

Other States of the Same Protein in the Database

Vpx protein

State in the Current Structure

Other States of the Same Protein in the Database

SAM domain and HD domain-containing protein

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4z8l__assembly_1__model_1

4z8l__assembly_1__model_1 | I(q)

4z8l__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of DCAF1/SIV-MND VPX/MND SAMHD1 NTD ternary complex

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

Protein VPRBP

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Vpx protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

SAM domain and HD domain-containing protein

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

4z8l__assembly_1__model_1

4z8l__assembly_1__model_1 | I(q)

4z8l__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)