SAXSdb — 3t98

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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 96	Nucleoporin Nup58/Nup45 × 32 （P70581） water × 96	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 A； PDBConstruct 2–51； UniProt 445–494 Author chain C； PDBConstruct 2–51； UniProt 445–494

Nucleoporin Nup58/Nup45

Rattus norvegicus

UniProt P70581

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 96	Nuclear pore complex protein Nup54 × 64 （P70582） water × 96	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NUPL1_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 5–93； UniProt 327–415

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	3t98
Deposition date deposition_date	2011-08-02
Structure title title	Molecular Architecture of the Transport Channel of the Nuclear Pore Complex: Nup54/Nup58
Keywords keywords	;Nup58, Nup54, Nup62 complex, nuclear import, coiled-coil, helix, hairpin, FG-repeat, nucleoporin, NPC, nuclear tranport, transport channel, Nup62, Nup45, Nup93, karyopherin, nuclear pore complex, nuclear pore domain, nuclear envelope, 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.

3t98__assembly_1__model_1

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

Download this curve (.dat)

3t98__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3t98__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	0.00 Å
Rg (electron density)	224.10 Å
Total Rg	223.30 Å
Atom count	42816
Residues	5152
Excluded volume	766670 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3t98__assembly_1__model_1`	96-meric （96）	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	6003.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	1394

MNHFGAVKSEEKYYIDADLLREIKQHLKQQQEGLSHLISIIKDDLEDIKLV

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	Nucleoporin Nup58/Nup45
Molecular weight formula_weight	10781.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSHMAPADYFRVLVQQFEVQLQQYRQQIEELENHLATQANNSHITPQDLSMAMQKIYQTFVALAAQLQSIHENVKVLKEQYLSYRKMFLGDAG

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	56

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3t98B00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1350 —

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Unit-cell length a length_a	54.960 Å
Unit-cell length b length_b	54.960 Å
Unit-cell length c length_c	190.290 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	16

Space group space_group	P 41 2 2
Space-group number int_tables_number	91
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2530
R_work r_work	0.2500
R_free r_free	0.2720

Molecular Architecture of the Transport Channel of the Nuclear Pore Complex: Nup54/Nup58

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

Nucleoporin Nup58/Nup45

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

3t98__assembly_1__model_1

3t98__assembly_1__model_1 | I(q)

3t98__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) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Molecular Architecture of the Transport Channel of the Nuclear Pore Complex: Nup54/Nup58

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

Nucleoporin Nup58/Nup45

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

3t98__assembly_1__model_1

3t98__assembly_1__model_1 | I(q)

3t98__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) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)