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8cqb

Cryo-EM structure of the human GBP1 dimer bound to GDP-AlF3

Method: ELECTRON MICROSCOPY Dmax: 132.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Guanylate-binding protein 1

Homo sapiens

UniProt P32455

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–592 Chain B； UniProt 1–592 Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 2 AF3 ALUMINUM FLUORIDE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4；5u mM HEPES pH7.4, 150 mM NaCl, 1 mM DTT, 200 uM GDP, 10 mM NaF, 300 uM AlCl3, 5 mM MgCl2 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.70 Å

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 8CQB Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1DG3 STRUCTURE OF HUMAN GUANYLATE BINDING PROTEIN-1 IN NUCLEOTIDE FREE FORM Deposited 1999-11-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–592（592 aa） Fragment：FULL LENGTH PROTEIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100MM MES-NAOH, 7.5% PEG6000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.80 Å R-free 0.276
1F5N HUMAN GUANYLATE BINDING PROTEIN-1 IN COMPLEX WITH THE GTP ANALOGUE, GMPPNP. Deposited 2000-06-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–592（592 aa）
Mutation：Q507H MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；15-20% PEG3350, 150-200mM MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Resolution 1.70 Å R-free 0.255
2B8W Crystal-structure of the N-terminal Large GTPase Domain of human Guanylate Binding protein 1 (hGBP1) in complex with GMP/AlF4 Deposited 2005-10-10 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–317（317 aa） Fragment：N-terminal Large GTPase domain
Chain B 1–317（317 aa） Fragment：N-terminal Large GTPase domain
Not recorded MG MAGNESIUM ION × 2 ALF TETRAFLUOROALUMINATE ION × 2 5GP GUANOSINE-5'-MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 298 K；5% PEG3350, 150 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.22 Å R-free 0.233
2B92 Crystal-structure of the N-terminal Large GTPase Domain of human Guanylate Binding protein 1 (hGBP1) in complex with GDP/AlF3 Deposited 2005-10-10 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–317（317 aa） Fragment：N-terminal Large GTPase domain
Chain B 1–317（317 aa） Fragment：N-terminal Large GTPase domain
Not recorded MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 AF3 ALUMINUM FLUORIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 298 K；12.5% Peg3350, 125mM Na2HPO4 (from Hampton Research peg/ion screen supplied at pH9.1), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.20 Å R-free 0.250
2BC9 Crystal-structure of the N-terminal large GTPase Domain of human Guanylate Binding protein 1 (hGBP1) in complex with non-hydrolysable GTP analogue GppNHp Deposited 2005-10-19 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–317（317 aa） Fragment：N-terminal Large GTPase doamin
Not recorded MG MAGNESIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；10 % Peg 3350, 100 mM NaSCN, 40 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.269
2D4H Crystal-structure of the N-terminal large GTPase Domain of human Guanylate Binding protein 1 (hGBP1) in complex with GMP Deposited 2005-10-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–317（317 aa） Fragment：N-terminal Large GTPase domain
Not recorded 5GP GUANOSINE-5'-MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 298 K；20% Peg 3350, 130 mM NH4NO3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.90 Å R-free 0.275
2D4H Crystal-structure of the N-terminal large GTPase Domain of human Guanylate Binding protein 1 (hGBP1) in complex with GMP Deposited 2005-10-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–317（317 aa） Fragment：N-terminal Large GTPase domain
Not recorded 5GP GUANOSINE-5'-MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 298 K；20% Peg 3350, 130 mM NH4NO3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.90 Å R-free 0.275
6K1Z Crystal structure of farnesylated hGBP1 Deposited 2019-05-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–592（592 aa）
Not recorded FAR FARNESYL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.02M Citric acid/0.08M BIS-TRIS propane (pH 8.8), 16% w/v Polyethylene glycol 3350
Resolution 2.31 Å R-free 0.267
6K2D The crystal structure of GBP1 with LRR domain of IpaH9.8 Deposited 2019-05-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–479（479 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1.6M Sodium/potassium phosphate pH 6.5
Resolution 3.60 Å R-free 0.287
6LOJ The complex structure of IpaH9.8-LRR and hGBP1 Deposited 2020-01-06 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 1–592（592 aa）
Mutation：Q507H GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；2.5M NaCl, 0.1M K/Na phosphate buffer, pH 6
Resolution 3.72 Å R-free 0.256
8Q4L GBP1 bound by 14-3-3sigma Deposited 2023-08-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 7–583（577 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8；150 mM KCl, 20 mM HEPES-KOH pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.12 Å

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

View Construct and Data Evidence
UniProt name GBP1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–592； UniProt 1–592 Author chain B； PDBConstruct 1–592； UniProt 1–592

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 8cqb

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8cqb
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8cqb
Deposition date deposition_date2023-03-04
Structure title titleCryo-EM structure of the human GBP1 dimer bound to GDP-AlF3
Keywords keywordsCell-autonomous immunity, intracellular pathogens, GTPase, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier37.54 Å
Radius of gyration Rg (electron density) rg_electron38.21 Å
Forward intensity I(0) i0183589000.00
Molecular weight molecular_weight109470.0 kDa
Excluded volume excluded_volume137150 ų
Envelope volume envelope_volume178930 ų
Hydration-shell volume shell_volume42119 ų
Envelope diameter envelope_diameter141.3 Å
Shell Rg shell_rg40.43 Å
Envelope Rg envelope_rg38.74 Å
Shape Rg shape_rg38.20 Å
Total Rg total_rg38.39 Å
Total atoms total_atoms7688
Residues n_residues956
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 dmax132.5 Å
Rg (real space) rg_real38.10 Å
Rg uncertainty (real space) rg_real_error1.38 Å
I(0) (real space) i0_real1.8360e+08
I(0) uncertainty (real space) i0_real_error3.4770e+06
Rg (reciprocal space) rg_reciprocal37.75 Å
I(0) (reciprocal space) i0_reciprocal183500000.0000
Solution quality estimate total_estimate0.7885
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.7 Å
Skewness Skewness skewness0.679
Kurtosis Kurtosis kurtosis-0.119
Angular range angular_range— – 0.2100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha30030000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.585; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.811; Smooth: 0.681
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)