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4lij

Crystal structure of a far upstream element (FUSE) binding protein 1 (FUBP1) from Homo sapiens at 1.95 A resolution

Method: X-RAY DIFFRACTION Dmax: 61.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Far upstream element-binding protein 1

Homo sapiens

UniProt Q96AE4

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 86–174 Chain B； UniProt 86–174 Chain C； UniProt 86–174 Fragment：UNP residues 86-174 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
2 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 86–174 Chain B； UniProt 86–174 Chain C； UniProt 86–174 Fragment：UNP residues 86-174 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

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 4LIJ 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 mutation/modification 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
6Y24 Crystal structure of fourth KH domain of FUBP1 Deposited 2020-02-14 Different construct Different mutation/modification Different oligomeric state 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
6Y2C Crystal structure of the third KH domain of FUBP1 Deposited 2020-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 260–350（91 aa）
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
6Y2C Crystal structure of the third KH domain of FUBP1 Deposited 2020-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 260–350（91 aa）
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
6Y2D Crystal structure of the second KH domain of FUBP1 Deposited 2020-02-15 Different construct Different mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification 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 —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–90； UniProt 86–174 Author chain B； PDBConstruct 2–90； UniProt 86–174 Author chain C； PDBConstruct 2–90； UniProt 86–174

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 4lij

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4lij
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4lij
Deposition date deposition_date2013-07-02
Structure title titleCrystal structure of a far upstream element (FUSE) binding protein 1 (FUBP1) from Homo sapiens at 1.95 A resolution
Keywords keywords;KH domain, PF00013, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, RNA-BINDING PROTEIN, Partnership for T-Cell Biology, TCELL, RNA BINDING PROTEIN ;; RNA BINDING PROTEIN
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_guinier19.45 Å
Radius of gyration Rg (electron density) rg_electron18.58 Å
Forward intensity I(0) i013581200.00
Molecular weight molecular_weight25406.0 kDa
Excluded volume excluded_volume30781 ų
Envelope volume envelope_volume37722 ų
Hydration-shell volume shell_volume17187 ų
Envelope diameter envelope_diameter63.8 Å
Shell Rg shell_rg24.43 Å
Envelope Rg envelope_rg18.70 Å
Shape Rg shape_rg18.60 Å
Total Rg total_rg19.33 Å
Total atoms total_atoms1735
Residues n_residues219
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 dmax61.2 Å
Rg (real space) rg_real19.35 Å
Rg uncertainty (real space) rg_real_error0.37 Å
I(0) (real space) i0_real1.3580e+07
I(0) uncertainty (real space) i0_real_error1.5520e+05
Rg (reciprocal space) rg_reciprocal19.37 Å
I(0) (reciprocal space) i0_reciprocal13580000.0000
Solution quality estimate total_estimate0.8283
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.3 Å
Skewness Skewness skewness0.157
Kurtosis Kurtosis kurtosis-0.474
Angular range angular_range— – 0.4100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1659000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000
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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) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd4lija_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.51 — Eukaryotic type KH-domain (KH-domain type I)
Superfamily Superfamily superfamilyd.51.1 — Eukaryotic type KH-domain (KH-domain type I)
Family Family familyd.51.1.1 — Eukaryotic type KH-domain (KH-domain type I)
Domain ID domain_idd4lijb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.51 — Eukaryotic type KH-domain (KH-domain type I)
Superfamily Superfamily superfamilyd.51.1 — Eukaryotic type KH-domain (KH-domain type I)
Family Family familyd.51.1.1 — Eukaryotic type KH-domain (KH-domain type I)
Domain ID domain_idd4lijc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.51 — Eukaryotic type KH-domain (KH-domain type I)
Superfamily Superfamily superfamilyd.51.1 — Eukaryotic type KH-domain (KH-domain type I)
Family Family familyd.51.1.1 — Eukaryotic type KH-domain (KH-domain type I)

CATH v4.4 (3 domains)

Domain ID domain_id4lijA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily10 — K Homology domain, type 1
Domain ID domain_id4lijB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily10 — K Homology domain, type 1
Domain ID domain_id4lijC00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily10 — K Homology domain, type 1
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8. Citations (1)

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9. Files and Curves (10)