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11bd

human nucleosome assembly protein 1 (human Nap1)

Method: X-RAY DIFFRACTION Dmax: 110.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nucleosome assembly protein 1-like 1

Homo sapiens

UniProt P55209

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 56–349 Chain B； UniProt 56–349 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；289.15 K；26% PEG 400, 0.1 M sodium citrate, pH 4.5, 0.1 M magnesium chloride hexahydrate, 0.1 M sodium chloride, 2% 1,4-dioxane Resolution 3.20 Å R-free 0.267

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 11BD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
11BC Human Nap1 in complex with HIV-1 Rev Deposited 2026-02-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–391（391 aa）
Chain B 1–391（391 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7UN3 Complex of UBE2O with NAP1L1 and ubiquitylated uL2 Deposited 2022-04-08 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 2–391（390 aa）
Chain C 2–391（390 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7UN6 Complex of UBE2O with NAP1L1 Deposited 2022-04-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–391（390 aa）
Chain C 2–391（390 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NP1L1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–295； UniProt 56–349 Author chain B； PDBConstruct 2–295； UniProt 56–349

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 11bd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 11bd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id11bd
Deposition date deposition_date2026-02-15
Structure title titlehuman nucleosome assembly protein 1 (human Nap1)
Keywords keywordsHistone, H2A-H2B, nucleosome assembly protein 1, nucleosome assembly protein like 1, CHAPERONE; CHAPERONE
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_guinier31.49 Å
Radius of gyration Rg (electron density) rg_electron30.54 Å
Forward intensity I(0) i069459100.00
Molecular weight molecular_weight65669.0 kDa
Excluded volume excluded_volume82134 ų
Envelope volume envelope_volume119490 ų
Hydration-shell volume shell_volume33297 ų
Envelope diameter envelope_diameter115.2 Å
Shell Rg shell_rg36.94 Å
Envelope Rg envelope_rg30.94 Å
Shape Rg shape_rg30.51 Å
Total Rg total_rg31.25 Å
Total atoms total_atoms4639
Residues n_residues578
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 dmax110.7 Å
Rg (real space) rg_real31.55 Å
Rg uncertainty (real space) rg_real_error1.27 Å
I(0) (real space) i0_real6.9460e+07
I(0) uncertainty (real space) i0_real_error1.1820e+06
Rg (reciprocal space) rg_reciprocal31.53 Å
I(0) (reciprocal space) i0_reciprocal69460000.0000
Solution quality estimate total_estimate0.8735
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.2 Å
Skewness Skewness skewness0.365
Kurtosis Kurtosis kurtosis-0.401
Angular range angular_range— – 0.2500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13300000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.806; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.946; Smooth: 0.989
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)