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3d8b

Crystal structure of human fidgetin-like protein 1 in complex with ADP

Method: X-RAY DIFFRACTION Dmax: 73.2 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Fidgetin-like protein 1

Homo sapiens

UniProt Q6PIW4

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 341–674 Chain B； UniProt 341–674 Fragment：AAA+ ATPase domain: Residues 341-674 ADP ADENOSINE-5'-DIPHOSPHATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；25% PEG 3350, 0.2M NaCl, 0.1M Bis-Tris, 0.02M ADP, 0.01M MgCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.00 Å R-free 0.237

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 3D8B Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8R64 Cryo-EM structure of the FIGNL1 AAA hexamer bound to RAD51 Deposited 2023-11-20 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 × 7 PDB declaration: heptameric
Chain A 284–674（391 aa）
Chain B 284–674（391 aa）
Chain C 284–674（391 aa）
Chain D 284–674（391 aa）
Chain E 284–674（391 aa）
Chain F 284–674（391 aa）
Mutation：E501Q Mutation：E501Q Mutation：E501Q Mutation：E501Q Mutation：E501Q Mutation：E501Q MG MAGNESIUM ION × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FIGL1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 24–357； UniProt 341–674 Author chain B； PDBConstruct 24–357； UniProt 341–674

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 3d8b

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3d8b
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3d8b
Deposition date deposition_date2008-05-23
Structure title titleCrystal structure of human fidgetin-like protein 1 in complex with ADP
Keywords keywords;AAA+, ATPase, ADP, SGC, Structural Genomics Consortium, ATP-binding, Hydrolase, Magnesium, Metal-binding, Nucleotide-binding, Phosphoprotein ;; HYDROLASE
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_guinier24.98 Å
Radius of gyration Rg (electron density) rg_electron23.89 Å
Forward intensity I(0) i064127000.00
Molecular weight molecular_weight62329.0 kDa
Excluded volume excluded_volume78189 ų
Envelope volume envelope_volume95346 ų
Hydration-shell volume shell_volume32059 ų
Envelope diameter envelope_diameter74.9 Å
Shell Rg shell_rg31.89 Å
Envelope Rg envelope_rg23.89 Å
Shape Rg shape_rg23.91 Å
Total Rg total_rg24.74 Å
Total atoms total_atoms4368
Residues n_residues555
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 dmax73.2 Å
Rg (real space) rg_real24.80 Å
Rg uncertainty (real space) rg_real_error0.33 Å
I(0) (real space) i0_real6.4130e+07
I(0) uncertainty (real space) i0_real_error7.3510e+05
Rg (reciprocal space) rg_reciprocal24.86 Å
I(0) (reciprocal space) i0_reciprocal64130000.0000
Solution quality estimate total_estimate0.9109
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary72.0 Å
Skewness Skewness skewness0.045
Kurtosis Kurtosis kurtosis-0.559
Angular range angular_range— – 0.3200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha20830000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.957; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.990
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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 (2 domains)

Domain ID domain_idd3d8ba_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.0 — automated matches
Domain ID domain_idd3d8bb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id3d8bA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id3d8bA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily60 —
Domain ID domain_id3d8bB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id3d8bB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily60 —
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8. Citations (1)

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9. Files and Curves (10)