3bg1

Architecture of a Coat for the Nuclear Pore Membrane

Method: X-RAY DIFFRACTION

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

Protein SEC13 homolog

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Nucleoporin NUP145 × 4 （P49687）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Nucleoporin NUP145 × 2 （P49687）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Nucleoporin NUP145 × 2 （P49687）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Nucleoporin NUP145 × 1 （P49687）	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Nucleoporin NUP145 × 1 （P49687）	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Nucleoporin NUP145 × 1 （P49687）	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	Nucleoporin NUP145 × 1 （P49687）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SEC13_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–316； UniProt 1–316 Author chain D； PDBConstruct 1–316； UniProt 1–316 Author chain E； PDBConstruct 1–316； UniProt 1–316 Author chain H； PDBConstruct 1–316； UniProt 1–316

Nucleoporin NUP145

Saccharomyces cerevisiae

UniProt P49687

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Protein SEC13 homolog × 4 （P55735）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Protein SEC13 homolog × 2 （P55735）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Protein SEC13 homolog × 2 （P55735）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Protein SEC13 homolog × 1 （P55735）	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Protein SEC13 homolog × 1 （P55735）	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Protein SEC13 homolog × 1 （P55735）	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	Protein SEC13 homolog × 1 （P55735）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NU145_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 15–442； UniProt 731–1158 Author chain C； PDBConstruct 15–442； UniProt 731–1158 Author chain F； PDBConstruct 15–442； UniProt 731–1158 Author chain G； PDBConstruct 15–442； UniProt 731–1158

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	3bg1
Deposition date deposition_date	2007-11-23
Structure title title	Architecture of a Coat for the Nuclear Pore Membrane
Keywords keywords	;NPC, Transport, WD repeat, Autocatalytic cleavage, mRNA transport, Nuclear pore complex, Nucleus, Phosphoprotein, RNA-binding, Translocation, PROTEIN TRANSPORT, HYDROLASE ;; PROTEIN TRANSPORT, HYDROLASE
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.

3bg1__assembly_1__model_1

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

Download this curve (.dat)

3bg1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bg1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	79.98 Å
Rg (electron density)	81.78 Å
Total Rg	81.08 Å
Atom count	22614
Residues	2822
Excluded volume	401810 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bg1__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3bg1__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3bg1__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3bg1__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3bg1__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3bg1__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3bg1__assembly_7__model_1`	dimeric （2）	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 (2)

Entity 1 Entity 1 polymer

Description description	Protein SEC13 homolog
Molecular weight formula_weight	34893.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,E,H
Atom count atom_count	22614

MVSVINTVDTSHEDMIHDAQMDYYGTRLATCSSDRSVKIFDVRNGGQILIADLRGHEGPVWQVAWAHPMYGNILASCSYDRKVIIWREENGTWEKSHEHAGHDSSVNSVCWAPHDYGLILACGSSDGAISLLTYTGEGQWEVKKINNAHTIGCNAVSWAPAVVPGSLIDHPSGQKPNYIKRFASGGCDNLIKLWKEEEDGQWKEEQKLEAHSDWVRDVAWAPSIGLPTSTIASCSQDGRVFIWTCDDASSNTWSPKLLHKFNDVVWHVSWSITANILAVSGGDNKVTLWKESVDGQWVCISDVNKGQGSVSASVTE

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Nucleoporin NUP145
Molecular weight formula_weight	50942.8 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,C,F,G

MGSSHHHHHHSGDPFSECNDEIDNAKLIMKERRFTASYTFAKFSTGSMLLTKDIVGKSGVSIKRLPTELQRKFLFDDVYLDKEIEKVTIEARKSNPYPQISESSLLFKDALDYMEKTSSDYNLWKLSSILFDPVSYPYKTDNDQVKMALLKKERHCRLTSWIVSQIGPEIEEKIRNSSNEIEQIFLYLLLNDVVRASKLAIESKNGHLSVLISYLGSNDPRIRDLAELQLQKWSTGGCSIDKNISKIYKLLSGSPFEGLFSLKELESEFSWLCLLNLTLCYGQIDEYSLESLVQSHLDKFSLPYDDPIGVIFQLYAANENTEKLYKEVRQRTNALDVQFCWYLIQTLRFNGTRVFSKETSDEATFAFAAQLEFAQLHGHSLFVSCFLNDDKAAEDTIKRLVMREITLLRASTNDHILNRLKIPSQLIFNAQALKDRYEGNYL

Source Source

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

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	3bg1A00
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	3bg1B01
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	50 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	3bg1B03
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	690 —

Domain ID domain_id	3bg1C01
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	50 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	3bg1C03
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	690 —

Domain ID domain_id	3bg1D00
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	3bg1E00
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	3bg1F01
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	50 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	3bg1F03
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	690 —

Domain ID domain_id	3bg1G01
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	50 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	3bg1G03
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	690 —

Domain ID domain_id	3bg1H00
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	181.367 Å
Unit-cell length b length_b	216.786 Å
Unit-cell length c length_c	192.578 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	32

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2490
R_work r_work	0.2490
R_free r_free	0.2940

Architecture of a Coat for the Nuclear Pore Membrane

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

Protein SEC13 homolog

State in the Current Structure

Other States of the Same Protein in the Database

Nucleoporin NUP145

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

3bg1__assembly_1__model_1

3bg1__assembly_1__model_1 | I(q)

3bg1__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Architecture of a Coat for the Nuclear Pore Membrane

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

Protein SEC13 homolog

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 NUP145

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

3bg1__assembly_1__model_1

3bg1__assembly_1__model_1 | I(q)

3bg1__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)