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3cqc

Nucleoporin Nup107/Nup133 interaction complex

Method: X-RAY DIFFRACTION Dmax: 100.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nuclear pore complex protein Nup107

Homo sapiens

UniProt P57740

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 658–925 Fragment：residues 658-925 Nuclear pore complex protein Nup133 × 1 （Q8WUM0） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；0.1M Hepes, 1.1M sodium malonate, 1-1.5% PEG MME 5000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K Resolution 2.53 Å R-free 0.245

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3CQC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3CQG Nucleoporin Nup107/Nup133 interaction complex, delta finger mutant Deposited 2008-04-02 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 658–771（114 aa） Fragment：residues 658-771, 802-925, connected by linker GGSGGS
Chain A 802–925（124 aa） Fragment：residues 658-771, 802-925, connected by linker GGSGGS
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；289 K；25-27% PEG 2000 MME, 500mM KSCN, 0.1M Hepes, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 3.00 Å R-free 0.287
3I4R Nup107(aa658-925)/Nup133(aa517-1156) complex, H.sapiens Deposited 2009-07-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 658–925（268 aa） Fragment：C-TERMINAL FRAGMENT (UNP residues 658-925)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；0.8 M sodium/potassium phosphate, 15 % glycerol, 2% PEG 3350, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.53 Å R-free 0.370
5A9Q Human nuclear pore complex Deposited 2015-07-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 304 PDB declaration: 304-meric
Chain 4 1–925（925 aa）
Chain D 1–925（925 aa）
Chain M 1–925（925 aa）
Chain V 1–925（925 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20MM TRIS, 0.2-0.4% TREHALOSE；pH 7.5；20MM TRIS, 0.2-0.4% TREHALOSE
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；VITRIFICATION 1 -- CRYOGEN- ETHANE-PROPANE MIXTURE, INSTRUMENT- HOMEMADE PLUNGER,
Resolution 23.00 Å
7PEQ Model of the outer rings of the human nuclear pore complex Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 288 PDB declaration: 288-meric
Chain AD 1–925（925 aa）
Chain BD 1–925（925 aa）
Chain CD 1–925（925 aa）
Chain DD 1–925（925 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE；Cells were grown on holey carbon, Au-mesh supports. Grids were rinsed briefly with PBS and manually blotted before plunging into liquid ethane.
Resolution 35.00 Å
7R5J Human nuclear pore complex (dilated) Deposited 2022-02-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 808 PDB declaration: 808-meric
Chain L0 1–925（925 aa）
Chain L1 1–925（925 aa）
Chain L2 1–925（925 aa）
Chain L3 1–925（925 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 50.00 Å
7R5K Human nuclear pore complex (constricted) Deposited 2022-02-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 808 PDB declaration: 808-meric
Chain L0 1–925（925 aa）
Chain L1 1–925（925 aa）
Chain L2 1–925（925 aa）
Chain L3 1–925（925 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 12.00 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NU107_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–270； UniProt 658–925

Nuclear pore complex protein Nup133

Homo sapiens

UniProt Q8WUM0

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 935–1156 Fragment：residues 935-1156 Nuclear pore complex protein Nup107 × 1 （P57740） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；0.1M Hepes, 1.1M sodium malonate, 1-1.5% PEG MME 5000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K Resolution 2.53 Å R-free 0.245

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3CQC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1XKS The crystal structure of the N-terminal domain of Nup133 reveals a beta-propeller fold common to several nucleoporins Deposited 2004-09-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 67–514（448 aa）
Mutation：F345L No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.7；277 K；PEG 3350, lithium sulfate, bis-tris, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K, pH 5.70
Resolution 2.35 Å R-free 0.236
3CQG Nucleoporin Nup107/Nup133 interaction complex, delta finger mutant Deposited 2008-04-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 934–1156（223 aa） Fragment：residues 935-1156
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；289 K；25-27% PEG 2000 MME, 500mM KSCN, 0.1M Hepes, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 3.00 Å R-free 0.287
3I4R Nup107(aa658-925)/Nup133(aa517-1156) complex, H.sapiens Deposited 2009-07-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 517–1156（640 aa） Fragment：HELICAL DOMAIN (UNP residues 517-1156)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；0.8 M sodium/potassium phosphate, 15 % glycerol, 2% PEG 3350, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.53 Å R-free 0.370
5A9Q Human nuclear pore complex Deposited 2015-07-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 304 PDB declaration: 304-meric
Chain 3 1–1156（1156 aa）
Chain C 1–1156（1156 aa）
Chain L 1–1156（1156 aa）
Chain U 1–1156（1156 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20MM TRIS, 0.2-0.4% TREHALOSE；pH 7.5；20MM TRIS, 0.2-0.4% TREHALOSE
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；VITRIFICATION 1 -- CRYOGEN- ETHANE-PROPANE MIXTURE, INSTRUMENT- HOMEMADE PLUNGER,
Resolution 23.00 Å
7PEQ Model of the outer rings of the human nuclear pore complex Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 288 PDB declaration: 288-meric
Chain AC 1–1156（1156 aa）
Chain BC 1–1156（1156 aa）
Chain CC 1–1156（1156 aa）
Chain DC 1–1156（1156 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE；Cells were grown on holey carbon, Au-mesh supports. Grids were rinsed briefly with PBS and manually blotted before plunging into liquid ethane.
Resolution 35.00 Å
7R5J Human nuclear pore complex (dilated) Deposited 2022-02-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 808 PDB declaration: 808-meric
Chain K0 1–1156（1156 aa）
Chain K1 1–1156（1156 aa）
Chain K2 1–1156（1156 aa）
Chain K3 1–1156（1156 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 50.00 Å
7R5K Human nuclear pore complex (constricted) Deposited 2022-02-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 808 PDB declaration: 808-meric
Chain K0 1–1156（1156 aa）
Chain K1 1–1156（1156 aa）
Chain K2 1–1156（1156 aa）
Chain K3 1–1156（1156 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 12.00 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NU133_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 6–227； UniProt 935–1156

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.

SAXS scattering curve SAXS Profile

SAXS profile for 3cqc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3cqc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3cqc
Deposition date deposition_date2008-04-02
Structure title titleNucleoporin Nup107/Nup133 interaction complex
Keywords keywordsNucleoporin, Nuclear Pore Complex, mRNA transport, Nucleus, Phosphoprotein, Protein transport, Translocation; PROTEIN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier28.08 Å
Radius of gyration Rg (electron density) rg_electron27.43 Å
Forward intensity I(0) i037737900.00
Molecular weight molecular_weight48762.0 kDa
Excluded volume excluded_volume61502 ų
Envelope volume envelope_volume81630 ų
Hydration-shell volume shell_volume26016 ų
Envelope diameter envelope_diameter103.6 Å
Shell Rg shell_rg32.92 Å
Envelope Rg envelope_rg27.99 Å
Shape Rg shape_rg27.48 Å
Total Rg total_rg27.86 Å
Total atoms total_atoms3431
Residues n_residues433
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax100.3 Å
Rg (real space) rg_real28.12 Å
Rg uncertainty (real space) rg_real_error1.01 Å
I(0) (real space) i0_real3.7740e+07
I(0) uncertainty (real space) i0_real_error6.3820e+05
Rg (reciprocal space) rg_reciprocal28.11 Å
I(0) (reciprocal space) i0_reciprocal37740000.0000
Solution quality estimate total_estimate0.8601
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.6 Å
Skewness Skewness skewness0.325
Kurtosis Kurtosis kurtosis-0.257
Angular range angular_range— – 0.2800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6037000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.787; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.852; Smooth: 0.964
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id3cqcA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology190 — Delta-Endotoxin; domain 1
Homologous superfamily homologous superfamily50 —
Domain ID domain_id3cqcB01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily1380 —
Domain ID domain_id3cqcB02
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily700 —
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8. Citations (1)

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9. Files and Curves (10)