SAXSdb — 7vpg

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

mRNA export factor

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	Isoform 3 of Nuclear pore complex protein Nup98-Nup96 × 1 （P52948） ORF6 protein × 1 （P59634） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Isoform 3 of Nuclear pore complex protein Nup98-Nup96 × 1 （P52948） ORF6 protein × 1 （P59634） water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Isoform 3 of Nuclear pore complex protein Nup98-Nup96 × 1 （P52948） ORF6 protein × 1 （P59634） water × 3	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Isoform 3 of Nuclear pore complex protein Nup98-Nup96 × 1 （P52948） ORF6 protein × 1 （P59634） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAE1L_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–368； UniProt 1–368 Author chain C； PDBConstruct 1–368； UniProt 1–368 Author chain E； PDBConstruct 1–368； UniProt 1–368 Author chain G； PDBConstruct 1–368； UniProt 1–368

Isoform 3 of Nuclear pore complex protein Nup98-Nup96

Homo sapiens

UniProt P52948

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	mRNA export factor × 1 （P78406） ORF6 protein × 1 （P59634） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	mRNA export factor × 1 （P78406） ORF6 protein × 1 （P59634） water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	mRNA export factor × 1 （P78406） ORF6 protein × 1 （P59634） water × 3	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	mRNA export factor × 1 （P78406） ORF6 protein × 1 （P59634） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NUP98_HUMAN
Isoform	P52948-3
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 12–67； UniProt 158–213 Author chain D； PDBConstruct 12–67； UniProt 158–213 Author chain F； PDBConstruct 12–67； UniProt 158–213 Author chain H； PDBConstruct 12–67； UniProt 158–213

ORF6 protein

OrganismNot specified

UniProt P59634

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	mRNA export factor × 1 （P78406） Isoform 3 of Nuclear pore complex protein Nup98-Nup96 × 1 （P52948） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	mRNA export factor × 1 （P78406） Isoform 3 of Nuclear pore complex protein Nup98-Nup96 × 1 （P52948） water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	mRNA export factor × 1 （P78406） Isoform 3 of Nuclear pore complex protein Nup98-Nup96 × 1 （P52948） water × 3	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	mRNA export factor × 1 （P78406） Isoform 3 of Nuclear pore complex protein Nup98-Nup96 × 1 （P52948） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NS6_SARS
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain I； PDBConstruct 1–22； UniProt 42–63 Author chain J； PDBConstruct 1–22； UniProt 42–63 Author chain K； PDBConstruct 1–22； UniProt 42–63 Author chain X； PDBConstruct 1–22； UniProt 42–63

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	7vpg
Deposition date deposition_date	2021-10-17
Structure title title	Crystal structure of the C-terminal tail of SARS-CoV-1 Orf6 complex with human nucleoporin pair Rae1-Nup98
Keywords keywords	Complex, Coronavirus, RNA nuclear export, VIRAL PROTEIN; VIRAL 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.

7vpg__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7vpg__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7vpg__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	21.17 Å
Rg (electron density)	19.97 Å
Total Rg	20.93 Å
Atom count	3144
Residues	396
Excluded volume	55329 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7vpg__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7vpg__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`7vpg__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`7vpg__assembly_4__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 (4)

Entity 1 Entity 1 polymer

Description description	mRNA export factor
Molecular weight formula_weight	42398.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	13136

MSLFGTTSGFGTSGTSMFGSATTDNHNPMKDIEVTSSPDDSIGCLSFSPPTLPGNFLIAGSWANDVRCWEVQDSGQTIPKAQQMHTGPVLDVCWSDDGSKVFTASCDKTAKMWDLSSNQAIQIAQHDAPVKTIHWIKAPNYSCVMTGSWDKTLKFWDTRSSNPMMVLQLPERCYCADVIYPMAVVATAERGLIVYQLENQPSEFRRIESPLKHQHRCVAIFKDKQNKPTGFALGSIEGRVAIHYINPPNPAKDNFTFKCHRSNGTNTSAPQDIYAVNGIAFHPVHGTLATVGSDGRFSFWDKDARTKLKTSEQLDQPISACCFNHNGNIFAYASSYDWSKGHEFYNPQKKNYIFLRNAAEELKPRNKKHHHHHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Isoform 3 of Nuclear pore complex protein Nup98-Nup96
Molecular weight formula_weight	7785.7 kDa
EC 编号 ec_number	3.4.21.-
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

MHHHHHHHHHHTGTTIKFNPPTGTDTMVKAGVSTNISTKHQCITAMKEYESKSLEELRLEDYQANRK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 polymer

Description description	ORF6 protein
Molecular weight formula_weight	2657.9 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X,I,J,K

KPLTKKNYSELDDEEPMELDYP

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	407

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	7vpgA01
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	7vpgC01
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	7vpgE01
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	7vpgG01
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

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Unit-cell length a length_a	149.614 Å
Unit-cell length b length_b	103.299 Å
Unit-cell length c length_c	134.936 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.96 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	2.490 Å
Low-resolution limit resolution_low	47.440 Å
R factor r_factor	0.1867
R_work r_work	0.1855
R_free r_free	0.2305

Crystal structure of the C-terminal tail of SARS-CoV-1 Orf6 complex with human nucleoporin pair Rae1-Nup98

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

mRNA export factor

State in the Current Structure

Other States of the Same Protein in the Database

Isoform 3 of Nuclear pore complex protein Nup98-Nup96

State in the Current Structure

Other States of the Same Protein in the Database

ORF6 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

7vpg__assembly_2__model_1

7vpg__assembly_2__model_1 | I(q)

7vpg__assembly_2__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 (4)

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

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the C-terminal tail of SARS-CoV-1 Orf6 complex with human nucleoporin pair Rae1-Nup98

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

mRNA export 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

Isoform 3 of Nuclear pore complex protein Nup98-Nup96

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ORF6 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

7vpg__assembly_2__model_1

7vpg__assembly_2__model_1 | I(q)

7vpg__assembly_2__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 (4)

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

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)