SAXSdb — 3pbp

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

Nucleoporin NUP82

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Nucleoporin NUP116/NSP116 × 1 （Q02630） Nucleoporin NUP159 × 1 （P40477）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Nucleoporin NUP116/NSP116 × 1 （Q02630） Nucleoporin NUP159 × 1 （P40477） TRIETHYLENE GLYCOL × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Nucleoporin NUP116/NSP116 × 1 （Q02630） Nucleoporin NUP159 × 1 （P40477）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Nucleoporin NUP116/NSP116 × 1 （Q02630） Nucleoporin NUP159 × 1 （P40477）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NUP82_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–452； UniProt 1–452 Author chain D； PDBConstruct 1–452； UniProt 1–452 Author chain G； PDBConstruct 1–452； UniProt 1–452 Author chain J； PDBConstruct 1–452； UniProt 1–452

Nucleoporin NUP116/NSP116

Saccharomyces cerevisiae

UniProt Q02630

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Nucleoporin NUP82 × 1 （P40368） Nucleoporin NUP159 × 1 （P40477）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Nucleoporin NUP82 × 1 （P40368） Nucleoporin NUP159 × 1 （P40477） TRIETHYLENE GLYCOL × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Nucleoporin NUP82 × 1 （P40368） Nucleoporin NUP159 × 1 （P40477）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Nucleoporin NUP82 × 1 （P40368） Nucleoporin NUP159 × 1 （P40477）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NU116_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–148； UniProt 967–1113 Author chain E； PDBConstruct 2–148； UniProt 967–1113 Author chain H； PDBConstruct 2–148； UniProt 967–1113 Author chain K； PDBConstruct 2–148； UniProt 967–1113

Nucleoporin NUP159

Saccharomyces cerevisiae

UniProt P40477

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Nucleoporin NUP82 × 1 （P40368） Nucleoporin NUP116/NSP116 × 1 （Q02630）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Nucleoporin NUP82 × 1 （P40368） Nucleoporin NUP116/NSP116 × 1 （Q02630） TRIETHYLENE GLYCOL × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Nucleoporin NUP82 × 1 （P40368） Nucleoporin NUP116/NSP116 × 1 （Q02630）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Nucleoporin NUP82 × 1 （P40368） Nucleoporin NUP116/NSP116 × 1 （Q02630）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NU159_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–36； UniProt 1425–1460 Author chain F； PDBConstruct 1–36； UniProt 1425–1460 Author chain I； PDBConstruct 1–36； UniProt 1425–1460 Author chain L； PDBConstruct 1–36； UniProt 1425–1460

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	3pbp
Deposition date deposition_date	2010-10-20
Structure title title	Structure of the yeast heterotrimeric Nup82-Nup159-Nup116 nucleoporin complex
Keywords keywords	;beta-propeller, nucleoporin, mRNA export, mRNP remodelling, NUCLEOCYTOPLASMIC Transport, PROTEIN TRANSPORT, TRANSLOCATION, TRANSPORT, autoproteolysis, Fusion protein, PROTOONCOGENE, ONCOPROTEIN, Protein COMPLEX, Nucleus, Nuclear Envelope, Nuclear Pore Complex, TRANSPORT PROTEIN, STRUCTURAL PROTEIN ;; TRANSPORT PROTEIN,STRUCTURAL 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.

3pbp__assembly_1__model_1

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

Download this curve (.dat)

3pbp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3pbp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.86 Å
Rg (electron density)	27.05 Å
Total Rg	27.74 Å
Atom count	4908
Residues	600
Excluded volume	88162 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3pbp__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3pbp__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3pbp__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3pbp__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	Nucleoporin NUP82
Molecular weight formula_weight	51982.5 kDa
Mutation mutation	C396S
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G,J
Atom count atom_count	19653

MSQSSRLSALPIFQASLSASQSPRYIFSSQNGTRIVFIQDNIIRWYNVLTDSLYHSLNFSRHLVLDDTFHVISSTSGDLLCLFNDNEIFVMEVPWGYSNVEDVSIQDAFQIFHYSIDEEEVGPKSSIKKVLFHPKSYRDSCIVVLKEDDTITMFDILNSQEKPIVLNKPNNSFGLDARVNDITDLEFSKDGLTLYCLNTTEGGDIFAFYPFLPSVLLLNEKDLNLILNKSLVMYESLDSTTDVIVKRNVIKQLQFVSKLHENWNSRFGKVDIQKEYRLAKVQGPFTINPFPGELYDYTATNIATILIDNGQNEIVCVSFDDGSLILLFKDLEMSMSWDVDNYVYNNSLVLIERVKLQREIKSLITLPEQLGKLYVISDNIIQQVNFMSWASTLSKSINESDLNPLAGLKFESKLEDIATIERIPNLAYINWNDQSNLALMSNKTLTFQNISS

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	Nucleoporin NUP116/NSP116
Molecular weight formula_weight	16832.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E,H,K

MNENYYISPSLDTLSSYSLLQLRKVPHLVVGHKSYGKIEFLEPVDLAGIPLTSLGGVIITFEPKTCIIYANLPNRPKRGEGINVRARITCFNCYPVDKSTRKPIKDPNHQLVKRHIERLKKNPNSKFESYDADSGTYVFIVNHAAEQT

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 polymer

Description description	Nucleoporin NUP159
Molecular weight formula_weight	4167.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F,I,L

SSITKDMKGFKVVEVGLAMNTKKQIGDFFKNLNMAK

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 4 Entity 4 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3pbpB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1610 — c-terminal autoproteolytic domain of nucleoporin nup98
Homologous superfamily homologous superfamily	10 — Peptidase S59, nucleoporin

Domain ID domain_id	3pbpE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1610 — c-terminal autoproteolytic domain of nucleoporin nup98
Homologous superfamily homologous superfamily	10 — Peptidase S59, nucleoporin

Domain ID domain_id	3pbpH00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1610 — c-terminal autoproteolytic domain of nucleoporin nup98
Homologous superfamily homologous superfamily	10 — Peptidase S59, nucleoporin

Domain ID domain_id	3pbpK00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1610 — c-terminal autoproteolytic domain of nucleoporin nup98
Homologous superfamily homologous superfamily	10 — Peptidase S59, nucleoporin

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Unit-cell length a length_a	61.503 Å
Unit-cell length b length_b	96.770 Å
Unit-cell length c length_c	144.282 Å
Unit-cell angle α angle_alpha	105.98 °
Unit-cell angle β angle_beta	93.97 °
Unit-cell angle γ angle_gamma	108.24 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2570
R_free r_free	0.2720

Structure of the yeast heterotrimeric Nup82-Nup159-Nup116 nucleoporin complex

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

Nucleoporin NUP82

State in the Current Structure

Other States of the Same Protein in the Database

Nucleoporin NUP116/NSP116

State in the Current Structure

Other States of the Same Protein in the Database

Nucleoporin NUP159

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

3pbp__assembly_1__model_1

3pbp__assembly_1__model_1 | I(q)

3pbp__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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Structure of the yeast heterotrimeric Nup82-Nup159-Nup116 nucleoporin complex

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

Nucleoporin NUP82

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 NUP116/NSP116

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 NUP159

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

3pbp__assembly_1__model_1

3pbp__assembly_1__model_1 | I(q)

3pbp__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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)