SAXSdb — 2ebq

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

Nuclear pore complex protein Nup153

Homo sapiens

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 722–761	Fragment：zf-RanBP domain	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition：1.21 mM 13C, 15N-labeled protein; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02%NaN3; 50uM ZnCl2+1mM IDA; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided

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 2EBQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2EBR Solution structure of the fourth zf-RanBP domain from human Nuclear pore complex protein Nup153 Deposited 2007-02-09	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 851–890（40 aa） Fragment：zf-RanBP domain	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.16 mM 13C, 15N-labeled protein; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02%NaN3; 50uM ZnCl2+1mM IDA; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2EBV Solution structure of the third zf-RanBP domain from human Nuclear pore complex protein Nup153 Deposited 2007-02-09	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 773–822（50 aa） Fragment：zf-RanBP domain	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.07mM 13C, 15N-labeled protein; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02%NaN3; 50uM ZnCl2+1mM IDA, 90%H2O, 10%D2O \| 90% H2O/10% D2O	Resolution not provided
2GQE Molecular characterization of the Ran binding zinc finger domain Deposited 2006-04-20	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 722–750（29 aa） Fragment：second zinc finger, residues 722-750	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 70mM, 20mM Tris, 50mM NaCl；Pressure AMBIENT NMR sample composition 1.3 mM hZnF2 U-15N, 13C, 20mM D-Tris, pH 7.0, 50mM NaCl, 1mM D-BME, 10 micromolr ZnCl2, 90%H2O, 10%D2O \| 90% H2O/10% D2O	Resolution not provided
4U0C Hexameric HIV-1 CA in complex with Nup153 peptide, P6 crystal form Deposited 2014-07-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: Dodecameric	Chain B 1407–1423（17 aa） Fragment：UNP residues 1407-1423	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；290 K；30% v/v PEG 400, 0.1 M CHES	Resolution 1.77 Å R-free 0.211
4U0D Hexameric HIV-1 CA in complex with Nup153 peptide, P212121 crystal form Deposited 2014-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: Nonameric	Chain M 1407–1423（17 aa） Fragment：UNP residues 1407-1423 Chain O 1407–1423（17 aa） Fragment：UNP residues 1407-1423 Chain P 1407–1423（17 aa） Fragment：UNP residues 1407-1423	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；290 K；10% w/v PEG 8K, 0.1M imidazole	Resolution 3.00 Å R-free 0.267
4U0D Hexameric HIV-1 CA in complex with Nup153 peptide, P212121 crystal form Deposited 2014-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: Nonameric	Chain N 1407–1423（17 aa） Fragment：UNP residues 1407-1423 Chain Q 1407–1423（17 aa） Fragment：UNP residues 1407-1423 Chain R 1407–1423（17 aa） Fragment：UNP residues 1407-1423	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；290 K；10% w/v PEG 8K, 0.1M imidazole	Resolution 3.00 Å R-free 0.267
5TSV HIV-1 CA hexamer with NUP153 peptide - R3 crystal form Deposited 2016-10-31	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain D 1365–1387（23 aa）	Not recorded	FLU 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M Tris, pH 8.2 12% PEG 8000 2% Tacsimate	Resolution 2.50 Å R-free 0.251
5TSX HIV-1 CA hexamer with NUP153 peptide - P1 crystal form Deposited 2016-10-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain M 1365–1387（23 aa） Chain P 1365–1387（23 aa） Chain R 1365–1387（23 aa）	Not recorded	FLU 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M Tris, pH 9 12% PEG 8000	Resolution 1.90 Å R-free 0.228
5TSX HIV-1 CA hexamer with NUP153 peptide - P1 crystal form Deposited 2016-10-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain N 1365–1387（23 aa） Chain O 1365–1387（23 aa） Chain T 1365–1387（23 aa）	Not recorded	FLU 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M Tris, pH 9 12% PEG 8000	Resolution 1.90 Å R-free 0.228
6AYA Structure of the native full-length HIV-1 capsid protein in complex with Nup153 peptide Deposited 2017-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 1407–1423（17 aa）	Not recorded	IOD IODIDE ION × 42 CL CHLORIDE ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG3350, NaI, MIB, Glycerol	Resolution 2.40 Å R-free 0.274
8CKY HIV-1 mature capsid hexamer from CA-IP6 CLPs, bound to Nup153 peptide Deposited 2023-02-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 1407–1423（17 aa） Fragment：UNP residues 1407-1423	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.1 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
8CL0 HIV-1 mature capsid hexamer next to pentamer (type I) from CA-IP6 CLPs bound to Nup153 peptide. Deposited 2023-02-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain G 1407–1423（17 aa） Fragment：UNP residues 1407-1423 Chain H 1407–1423（17 aa） Fragment：UNP residues 1407-1423 Chain I 1407–1423（17 aa） Fragment：UNP residues 1407-1423 Chain J 1407–1423（17 aa） Fragment：UNP residues 1407-1423 Chain K 1407–1423（17 aa） Fragment：UNP residues 1407-1423 Chain L 1407–1423（17 aa） Fragment：UNP residues 1407-1423	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.1 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.12 Å
9CNU HIV-2 CA hexamer bound with Nup153 peptide; assembled with liposome templating Deposited 2024-07-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 1411–1425（15 aa） Chain B 1464–1475（12 aa）	Mutation：Delta(1-1410) and Delta(1426-1463) Mutation：Delta(1-1410) and Delta(1426-1463)	IHP INOSITOL HEXAKISPHOSPHATE × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7；The mixed buffer of storage buffer for the protein and lipid components with IP6 supplemented. cryo-EM vitrification conditions Cryogen ETHANE；Grids were dual-side blotted with blot force 0 for 5.5 sec before plunge freezing in liquid ethane.	Resolution 2.99 Å
9CNU HIV-2 CA hexamer bound with Nup153 peptide; assembled with liposome templating Deposited 2024-07-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1411–1425（15 aa） Chain B 1464–1475（12 aa）	Mutation：Delta(1-1410) and Delta(1426-1463) Mutation：Delta(1-1410) and Delta(1426-1463)	IHP INOSITOL HEXAKISPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7；The mixed buffer of storage buffer for the protein and lipid components with IP6 supplemented. cryo-EM vitrification conditions Cryogen ETHANE；Grids were dual-side blotted with blot force 0 for 5.5 sec before plunge freezing in liquid ethane.	Resolution 2.99 Å

11 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NU153_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–47； UniProt 722–761

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	2ebq
Deposition date deposition_date	2007-02-09
Structure title title	Solution structure of the second zf-RanBP domain from human Nuclear pore complex protein Nup153
Keywords keywords	;zf-RanBP domain, Nuclear pore complex protein, Nucleoporin Nup153, 153 kDa nucleoporin, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, TRANSPORT PROTEIN ;; TRANSPORT PROTEIN
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	13.37 Å
Radius of gyration Rg (electron density) rg_electron	13.36 Å
Forward intensity I(0) i0	159124000.00
Molecular weight molecular_weight	97519.0 kDa
Excluded volume excluded_volume	119440 Å³
Envelope volume envelope_volume	39390 Å³
Hydration-shell volume shell_volume	17725 Å³
Envelope diameter envelope_diameter	66.7 Å
Shell Rg shell_rg	25.05 Å
Envelope Rg envelope_rg	19.43 Å
Shape Rg shape_rg	13.36 Å
Total Rg total_rg	13.99 Å
Total atoms total_atoms	13340
Residues n_residues	940
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	34.4 Å
Rg (real space) rg_real	12.56 Å
Rg uncertainty (real space) rg_real_error	0.06 Å
I(0) (real space) i0_real	1.5190e+08
I(0) uncertainty (real space) i0_real_error	1.2130e+06
Rg (reciprocal space) rg_reciprocal	13.53 Å
I(0) (reciprocal space) i0_reciprocal	159100000.0000
Solution quality estimate total_estimate	0.6696
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	11.3 Å
Skewness Skewness skewness	0.238
Kurtosis Kurtosis kurtosis	-0.846
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	4.5850
Highest regularization parameter α highest_alpha	28950.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.003; Oscil: 1.000; Stabil: 0.983; Sysdev: 0.000; Positv: 1.000; Valcen: 0.757; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2ebqA00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1060 — ZNF265 like
Homologous superfamily homologous superfamily	10 — Zinc finger, RanBP2-type

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8. Citations (1)

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Description description	Nuclear pore complex protein Nup153
Molecular weight formula_weight	4831.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	13340

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

fit	/app/data/saxs_computation/eb/2ebq/2ebq.fit
pddf	/app/data/pr_computation/eb/2ebq/2ebq.pr.out
profile	/app/data/saxs_computation/eb/2ebq/2ebq.dat

Solution structure of the second zf-RanBP domain from human Nuclear pore complex protein Nup153

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

Nuclear pore complex protein Nup153

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)