SAXSdb — 6y2c

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

Far upstream element-binding protein 1

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 260–350	Not recorded	EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；10% PEG 6000, 10% ethylene glycol, 0.015M Zinkchlorid, 0.1 M MES, pH 6.0	Resolution 2.00 Å R-free 0.240
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 260–350	Not recorded	EDO 1,2-ETHANEDIOL × 6 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；10% PEG 6000, 10% ethylene glycol, 0.015M Zinkchlorid, 0.1 M MES, pH 6.0	Resolution 2.00 Å R-free 0.240

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 6Y2C	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1J4W COMPLEX OF THE KH3 and KH4 DOMAINS OF FBP WITH A SINGLE_STRANDED 29mer DNA OLIGONUCLEOTIDE FROM THE FUSE ELEMENT OF THE C-MYC ONCOGENE Deposited 2001-11-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 278–447（170 aa） Fragment：RESIDUES 278-447, NUMBERERED 5-174. KH3 AND KH4 DOMAINS.	Mutation：C59A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；308 K；Ionic strength (raw mmCIF value) 50 mM SODIUM PHOSPHATE	Resolution not provided
2KXH Solution structure of the first two RRM domains of FIR in the complex with FBP Nbox peptide Deposited 2010-05-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 27–52（26 aa） Fragment：UNP residues 27-52	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 8；310 K；Ionic strength (raw mmCIF value) 0.06；Pressure ambient NMR measurement conditions pH 8；318 K；Ionic strength (raw mmCIF value) 0.06；Pressure ambient NMR sample composition 0.6 mM [U-15N] protein_1-1, 10 mM TRIS-HCl pH 8.0-2, 50 mM sodium chloride-3, 2 mM TCEP-4, 1.25 mM protein_2-5, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition mM [U-13C; U-15N] protein_1-6, 10 mM TRIS-HCl pH 8.0-7, 50 mM sodium chloride-8, 2 mM TCEP-9, mM protein_2-10, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.3 mM [U-13C; U-15N] protein_2-11, 10 mM TRIS-HCl pH 8.0-12, 50 mM sodium chloride-13, 2 mM TCEP-14, mM protein_1-15, 100% D2O \| 100% D2O NMR sample composition mM [U-13C; U-15N] protein_1-16, 10 mM TRIS-HCl pH 8.0-17, 50 mM sodium chloride-18, 2 mM TCEP-19, mM protein_2-20, 100% D2O \| 100% D2O	Resolution not provided
4LIJ Crystal structure of a far upstream element (FUSE) binding protein 1 (FUBP1) from Homo sapiens at 1.95 A resolution Deposited 2013-07-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 86–174（89 aa） Fragment：UNP residues 86-174 Chain B 86–174（89 aa） Fragment：UNP residues 86-174 Chain C 86–174（89 aa） Fragment：UNP residues 86-174	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；20.00% Glycerol, 1.60M ammonium dihydrogen phosphate, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.80 Å R-free 0.199
4LIJ Crystal structure of a far upstream element (FUSE) binding protein 1 (FUBP1) from Homo sapiens at 1.95 A resolution Deposited 2013-07-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 86–174（89 aa） Fragment：UNP residues 86-174 Chain B 86–174（89 aa） Fragment：UNP residues 86-174 Chain C 86–174（89 aa） Fragment：UNP residues 86-174	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；20.00% Glycerol, 1.60M ammonium dihydrogen phosphate, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.80 Å R-free 0.199
6Y24 Crystal structure of fourth KH domain of FUBP1 Deposited 2020-02-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 365–455（91 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；3.1 M sodium formate	Resolution 1.86 Å R-free 0.243
6Y2D Crystal structure of the second KH domain of FUBP1 Deposited 2020-02-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 185–259（75 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2M ammonium sulfate, 5% 2-propanol, 2.5% Glycerol	Resolution 1.90 Å R-free 0.239
6Y2D Crystal structure of the second KH domain of FUBP1 Deposited 2020-02-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 185–259（75 aa）	Not recorded	SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2M ammonium sulfate, 5% 2-propanol, 2.5% Glycerol	Resolution 1.90 Å R-free 0.239
6Y2D Crystal structure of the second KH domain of FUBP1 Deposited 2020-02-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 185–259（75 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2M ammonium sulfate, 5% 2-propanol, 2.5% Glycerol	Resolution 1.90 Å R-free 0.239
6Y2D Crystal structure of the second KH domain of FUBP1 Deposited 2020-02-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 185–259（75 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2M ammonium sulfate, 5% 2-propanol, 2.5% Glycerol	Resolution 1.90 Å R-free 0.239
8P25 Solution structure of a chimeric U2AF2 RRM2 / FUBP1 N-Box Deposited 2023-05-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–56（36 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50mM NaCl；Pressure 1 NMR sample composition 0.6 mM [U-100% 13C; U-100% 15N] Chimeric construct of U2AF2 linker-RRM2 and FUBP1 N-box, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.6 mM [U-100% 13C; U-100% 15N] Chimeric construct of U2AF2 linker-RRM2 and FUBP1 N-box, 100% D2O \| 100% D2O	Resolution not provided

6 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FUBP1_HUMAN
Isoform	Q96AE4-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–93； UniProt 260–350 Author chain B； PDBConstruct 3–93； UniProt 260–350

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	6y2c
Deposition date deposition_date	2020-02-15
Structure title title	Crystal structure of the third KH domain of FUBP1
Keywords keywords	ssDNA/RNA binding motif, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	17.88 Å
Radius of gyration Rg (electron density) rg_electron	16.68 Å
Forward intensity I(0) i0	6403830.00
Molecular weight molecular_weight	17687.0 kDa
Excluded volume excluded_volume	21916 Å³
Envelope volume envelope_volume	25496 Å³
Hydration-shell volume shell_volume	13497 Å³
Envelope diameter envelope_diameter	62.2 Å
Shell Rg shell_rg	21.77 Å
Envelope Rg envelope_rg	16.90 Å
Shape Rg shape_rg	16.67 Å
Total Rg total_rg	17.62 Å
Total atoms total_atoms	1228
Residues n_residues	156
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	60.1 Å
Rg (real space) rg_real	17.86 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	6.4040e+06
I(0) uncertainty (real space) i0_real_error	7.8190e+04
Rg (reciprocal space) rg_reciprocal	17.87 Å
I(0) (reciprocal space) i0_reciprocal	6404000.0000
Solution quality estimate total_estimate	0.7998
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	21.9 Å
Skewness Skewness skewness	0.313
Kurtosis Kurtosis kurtosis	-0.253
Angular range angular_range	— – 0.4450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	772600.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.800; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Far upstream element-binding protein 1
Molecular weight formula_weight	10183.5 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	1256

SMFREVRNEYGSRIGGNEGIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRCQHAAEIITDLLRSVQAGNP

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	8

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	28

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d6y2ca_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.51 — Eukaryotic type KH-domain (KH-domain type I)
Superfamily Superfamily superfamily	d.51.1 — Eukaryotic type KH-domain (KH-domain type I)
Family Family family	d.51.1.0 — automated matches

Domain ID domain_id	d6y2cb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.51 — Eukaryotic type KH-domain (KH-domain type I)
Superfamily Superfamily superfamily	d.51.1 — Eukaryotic type KH-domain (KH-domain type I)
Family Family family	d.51.1.0 — automated matches

Domain ID domain_id	d6y2cb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	6y2cA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — K Homology domain, type 1

Domain ID domain_id	6y2cB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — K Homology domain, type 1

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8. Citations (1)

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Unit-cell length a length_a	47.409 Å
Unit-cell length b length_b	47.409 Å
Unit-cell length c length_c	147.893 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	41.090 Å
R factor r_factor	0.2050
R_work r_work	0.2030
R_free r_free	0.2401

fit	/app/data/saxs_computation/y2/6y2c/6y2c.fit
pddf	/app/data/pr_computation/y2/6y2c/6y2c.pr.out
profile	/app/data/saxs_computation/y2/6y2c/6y2c.dat

Crystal structure of the third KH domain of FUBP1

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

Far upstream element-binding protein 1

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

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction