SAXSdb — 3lcn

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

Nuclear polyadenylated RNA-binding protein NAB2

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	mRNA transport factor GFD1 × 1 （Q04839） ZINC ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	mRNA transport factor GFD1 × 1 （Q04839） ZINC ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 8	mRNA transport factor GFD1 × 4 （Q04839） ZINC ION × 6 water × 8	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	mRNA transport factor GFD1 × 2 （Q04839） ZINC ION × 3 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NAB2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–105； UniProt 1–105 Author chain B； PDBConstruct 1–105； UniProt 1–105

mRNA transport factor GFD1

Saccharomyces cerevisiae

UniProt Q04839

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Nuclear polyadenylated RNA-binding protein NAB2 × 1 （P32505） ZINC ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Nuclear polyadenylated RNA-binding protein NAB2 × 1 （P32505） ZINC ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 8	Nuclear polyadenylated RNA-binding protein NAB2 × 4 （P32505） ZINC ION × 6 water × 8	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	Nuclear polyadenylated RNA-binding protein NAB2 × 2 （P32505） ZINC ION × 3 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GFD1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–29； UniProt 123–151 Author chain D； PDBConstruct 1–29； UniProt 123–151

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	3lcn
Deposition date deposition_date	2010-01-11
Structure title title	Nab2:Gfd1 complex
Keywords keywords	;nuclear mRNA export, Metal-binding, Nucleus, RNA-binding, Zinc-finger, Membrane, mRNA transport, Nuclear pore complex, Phosphoprotein, Protein transport, Translocation, Transport, NUCLEAR PROTEIN ;; NUCLEAR 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.

3lcn__assembly_1__model_1

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

Download this curve (.dat)

3lcn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3lcn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.24 Å
Rg (electron density)	14.62 Å
Total Rg	15.93 Å
Atom count	1926
Residues	121
Excluded volume	17161 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3lcn__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3lcn__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3lcn__assembly_3__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3lcn__assembly_4__model_1`	tetrameric （4）	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	Nuclear polyadenylated RNA-binding protein NAB2
Molecular weight formula_weight	11461.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3920

MSQEQYTENLKVIVAEKLAGIPNFNEDIKYVAEYIVLLIVNGGTVESVVDELASLFDSVSRDTLANVVQTAFFALEALQQGESAENIVSKIRMMNAQSLGQSDIA

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	mRNA transport factor GFD1
Molecular weight formula_weight	3543.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

KQDTASKMKLLKKKIEEQREILQKTHHKN

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	89

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3lcnA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	340 — Endonuclease III; domain 1
Homologous superfamily homologous superfamily	40 — Nuclear abundant poly(A) RNA-bind protein 2, N-terminal domain

Domain ID domain_id	3lcnB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	340 — Endonuclease III; domain 1
Homologous superfamily homologous superfamily	40 — Nuclear abundant poly(A) RNA-bind protein 2, N-terminal domain

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Unit-cell length a length_a	55.833 Å
Unit-cell length b length_b	121.762 Å
Unit-cell length c length_c	37.376 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	19.073 Å
R factor r_factor	0.1891
R_work r_work	0.1871
R_free r_free	0.2263

Nab2:Gfd1 complex

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

Nuclear polyadenylated RNA-binding protein NAB2

State in the Current Structure

Other States of the Same Protein in the Database

mRNA transport factor GFD1

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

3lcn__assembly_1__model_1

3lcn__assembly_1__model_1 | I(q)

3lcn__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Nab2:Gfd1 complex

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

Nuclear polyadenylated RNA-binding protein NAB2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

mRNA transport factor GFD1

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

3lcn__assembly_1__model_1

3lcn__assembly_1__model_1 | I(q)

3lcn__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)