SAXSdb — 3t97

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

Nuclear pore complex protein Nup54

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Nuclear pore glycoprotein p62 × 2 （P17955） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NUP54_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 4–65； UniProt 346–407

Nuclear pore glycoprotein p62

Rattus norvegicus

UniProt P17955

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Nuclear pore complex protein Nup54 × 1 （P70582） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NUP62_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–64； UniProt 362–425 Author chain C； PDBConstruct 1–64； UniProt 362–425

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	3t97
Deposition date deposition_date	2011-08-02
Structure title title	Molecular Architecture of the Transport Channel of the Nuclear Pore Complex: Nup62/Nup54
Keywords keywords	;nucleoporin, coiled-coil, nuclear pore complex, central transport channel, alpha helical proteins, triple helix, buried polar residues, structural proteins, nucleoporins, FG repeat, nucleocytoplasmic transport, Nup58, Nup88, Nup93, karyopherin, nuclear envelope, nuclear pore membrane domain, central channel, PROTEIN TRANSPORT ;; PROTEIN TRANSPORT
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.

3t97__assembly_1__model_1

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

Download this curve (.dat)

3t97__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3t97__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.80 Å
Rg (electron density)	25.16 Å
Total Rg	25.40 Å
Atom count	1405
Residues	168
Excluded volume	25075 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3t97__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	Nuclear pore complex protein Nup54
Molecular weight formula_weight	7624.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	1434

GSHMTKQHQTRLDIISEDISELQKNQTTTMAKIAQYKRKLMDLSHRTLQVLIKQEIQRKSGYAIQ

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Nuclear pore glycoprotein p62
Molecular weight formula_weight	7537.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

NAWDRTLIENGEKITSLHREVEKVKLDQKRLDQELDFILSQQKELEDLLSPLEESVKEQSGTIY

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	29

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	3t97A00
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	170 —

Domain ID domain_id	3t97B00
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	490 — Single helix bin

Domain ID domain_id	3t97C00
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	170 —

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Unit-cell length a length_a	25.010 Å
Unit-cell length b length_b	62.350 Å
Unit-cell length c length_c	121.340 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2305
R_work r_work	0.2353
R_free r_free	0.2710

Molecular Architecture of the Transport Channel of the Nuclear Pore Complex: Nup62/Nup54

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

Nuclear pore complex protein Nup54

State in the Current Structure

Other States of the Same Protein in the Database

Nuclear pore glycoprotein p62

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

3t97__assembly_1__model_1

3t97__assembly_1__model_1 | I(q)

3t97__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Molecular Architecture of the Transport Channel of the Nuclear Pore Complex: Nup62/Nup54

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

Nuclear pore complex protein Nup54

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Nuclear pore glycoprotein p62

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

3t97__assembly_1__model_1

3t97__assembly_1__model_1 | I(q)

3t97__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)