SAXSdb — 11bc

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

Nucleosome assembly protein 1-like 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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 1–391 Chain B； UniProt 1–391	Not recorded	Protein Rev × 4 （Q76PP8）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.30 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 11BC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
11BD human nucleosome assembly protein 1 (human Nap1) Deposited 2026-02-15	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 56–349（294 aa） Chain B 56–349（294 aa）	Not recorded	No recorded non-water small molecule	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
7UN3 Complex of UBE2O with NAP1L1 and ubiquitylated uL2 Deposited 2022-04-08	Different construct Different oligomeric state 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 conditions	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 1–391； UniProt 1–391 Author chain B； PDBConstruct 1–391； UniProt 1–391

Protein Rev

Human immunodeficiency virus 1

UniProt Q76PP8

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain C； UniProt 1–116 Chain D； UniProt 1–116 Chain E； UniProt 1–116 Chain F； UniProt 1–116	Not recorded	Nucleosome assembly protein 1-like 1 × 2 （P55209）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.30 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 11BC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
11BE HIV-1 Rev Filament Deposited 2026-02-15	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 155 PDB declaration: 155-meric	Chain A1 1–116（116 aa） Chain A4 1–116（116 aa） Chain A5 1–116（116 aa） Chain A9 1–116（116 aa） Chain B1 1–116（116 aa） Chain B4 1–116（116 aa） Chain B5 1–116（116 aa） Chain B9 1–116（116 aa） Chain C1 1–116（116 aa） Chain C5 1–116（116 aa） Chain C6 1–116（116 aa） Chain C9 1–116（116 aa） Chain D1 1–116（116 aa） Chain D5 1–116（116 aa） Chain D6 1–116（116 aa） Chain D9 1–116（116 aa） Chain E1 1–116（116 aa） Chain E5 1–116（116 aa） Chain E6 1–116（116 aa） Chain E9 1–116（116 aa） Chain F1 1–116（116 aa） Chain F5 1–116（116 aa） Chain F6 1–116（116 aa） Chain F9 1–116（116 aa） Chain G1 1–116（116 aa） Chain G5 1–116（116 aa） Chain G6 1–116（116 aa） Chain G9 1–116（116 aa） Chain H1 1–116（116 aa） Chain H5 1–116（116 aa） Chain H6 1–116（116 aa） Chain H9 1–116（116 aa） Chain I1 1–116（116 aa） Chain I4 1–116（116 aa） Chain I9 1–116（116 aa） Chain J1 1–116（116 aa） Chain J4 1–116（116 aa） Chain J9 1–116（116 aa） Chain K1 1–116（116 aa） Chain K4 1–116（116 aa） Chain K9 1–116（116 aa） Chain L1 1–116（116 aa） Chain L4 1–116（116 aa） Chain L9 1–116（116 aa） Chain M1 1–116（116 aa） Chain M4 1–116（116 aa） Chain M5 1–116（116 aa） Chain M9 1–116（116 aa） Chain N1 1–116（116 aa） Chain N4 1–116（116 aa） Chain N5 1–116（116 aa） Chain N9 1–116（116 aa） Chain O1 1–116（116 aa） Chain O4 1–116（116 aa） Chain O5 1–116（116 aa） Chain O9 1–116（116 aa） Chain P1 1–116（116 aa） Chain P5 1–116（116 aa） Chain P9 1–116（116 aa） Chain R1 1–116（116 aa） Chain R4 1–116（116 aa） Chain R9 1–116（116 aa） Chain S1 1–116（116 aa） Chain S4 1–116（116 aa） Chain S9 1–116（116 aa） Chain T1 1–116（116 aa） Chain T4 1–116（116 aa） Chain T5 1–116（116 aa） Chain T9 1–116（116 aa） Chain U1 1–116（116 aa） Chain U4 1–116（116 aa） Chain U5 1–116（116 aa） Chain U9 1–116（116 aa） Chain V1 1–116（116 aa） Chain V5 1–116（116 aa） Chain V6 1–116（116 aa） Chain V9 1–116（116 aa） Chain W1 1–116（116 aa） Chain W5 1–116（116 aa） Chain W6 1–116（116 aa） Chain W9 1–116（116 aa） Chain X1 1–116（116 aa） Chain X5 1–116（116 aa） Chain X6 1–116（116 aa） Chain X9 1–116（116 aa） Chain Y1 1–116（116 aa） Chain Y5 1–116（116 aa） Chain Y6 1–116（116 aa） Chain Y9 1–116（116 aa） Chain a3 1–116（116 aa） Chain a7 1–116（116 aa） Chain a8 1–116（116 aa） Chain b3 1–116（116 aa） Chain b7 1–116（116 aa） Chain b8 1–116（116 aa） Chain c2 1–116（116 aa） Chain c7 1–116（116 aa） Chain c8 1–116（116 aa） Chain d2 1–116（116 aa） Chain d7 1–116（116 aa） Chain d8 1–116（116 aa） Chain e2 1–116（116 aa） Chain e7 1–116（116 aa） Chain e8 1–116（116 aa） Chain f2 1–116（116 aa） Chain f7 1–116（116 aa） Chain f8 1–116（116 aa） Chain g2 1–116（116 aa） Chain g7 1–116（116 aa） Chain g8 1–116（116 aa） Chain h2 1–116（116 aa） Chain h7 1–116（116 aa） Chain h8 1–116（116 aa） Chain i3 1–116（116 aa） Chain i7 1–116（116 aa） Chain j3 1–116（116 aa） Chain j7 1–116（116 aa） Chain k3 1–116（116 aa） Chain k7 1–116（116 aa） Chain l3 1–116（116 aa） Chain l7 1–116（116 aa） Chain m3 1–116（116 aa） Chain m7 1–116（116 aa） Chain m8 1–116（116 aa） Chain n3 1–116（116 aa） Chain n7 1–116（116 aa） Chain n8 1–116（116 aa） Chain o3 1–116（116 aa） Chain o7 1–116（116 aa） Chain o8 1–116（116 aa） Chain p3 1–116（116 aa） Chain p7 1–116（116 aa） Chain p8 1–116（116 aa） Chain r3 1–116（116 aa） Chain r7 1–116（116 aa） Chain s3 1–116（116 aa） Chain s7 1–116（116 aa） Chain t3 1–116（116 aa） Chain t7 1–116（116 aa） Chain t8 1–116（116 aa） Chain u3 1–116（116 aa） Chain u7 1–116（116 aa） Chain u8 1–116（116 aa） Chain v2 1–116（116 aa） Chain v7 1–116（116 aa） Chain v8 1–116（116 aa） Chain w2 1–116（116 aa） Chain w7 1–116（116 aa） Chain w8 1–116（116 aa） Chain x2 1–116（116 aa） Chain x7 1–116（116 aa） Chain x8 1–116（116 aa） Chain y2 1–116（116 aa） Chain y7 1–116（116 aa） Chain y8 1–116（116 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.30 Å
5DHV HIV-1 Rev NTD dimers with variable crossing angles Deposited 2015-08-31	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 × 3 PDB declaration: trimeric	Chain N 1–65（65 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystals of scFv-Rev were initially grown in 20% PEG 3350, a variety of salts (200 mM sodium sulfate, sodium bromide, or ammonium phosphate dibasic), and pH ranging from 6.5-8.5.	Resolution 2.30 Å R-free 0.227
5DHV HIV-1 Rev NTD dimers with variable crossing angles Deposited 2015-08-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain M 1–65（65 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystals of scFv-Rev were initially grown in 20% PEG 3350, a variety of salts (200 mM sodium sulfate, sodium bromide, or ammonium phosphate dibasic), and pH ranging from 6.5-8.5.	Resolution 2.30 Å R-free 0.227
5DHY HIV-1 Rev NTD dimers with variable crossing angles Deposited 2015-08-31	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–65（65 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystals of scFv-Rev were initially grown in 20% PEG 3350, a variety of salts (200 mM sodium sulfate, sodium bromide, or ammonium phosphate dibasic), and pH ranging from 6.5-8.5	Resolution 3.10 Å R-free 0.300
5DHY HIV-1 Rev NTD dimers with variable crossing angles Deposited 2015-08-31	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain M 1–65（65 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystals of scFv-Rev were initially grown in 20% PEG 3350, a variety of salts (200 mM sodium sulfate, sodium bromide, or ammonium phosphate dibasic), and pH ranging from 6.5-8.5	Resolution 3.10 Å R-free 0.300
5DHZ HIV-1 Rev NTD dimers with variable crossing angles Deposited 2015-08-31	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain M 1–65（65 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystals of scFv-Rev were initially grown in 20% PEG 3350, a variety of salts (200 mM sodium sulfate, sodium bromide, or ammonium phosphate dibasic), and pH ranging from 6.5-8.5	Resolution 4.30 Å R-free 0.324
6BSY HIV-1 Rev assembly domain (residues 1-69) Deposited 2017-12-04	Different construct Different mutation/modification Different oligomeric state 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 1–70（70 aa） Fragment：assembly domain (UNP residues 1-70) Chain B 1–70（70 aa） Fragment：assembly domain (UNP residues 1-70)	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；283.15 K；0.1 M sodium citrate, 25% MPD	Resolution 2.25 Å R-free 0.260
6CF2 Crystal structure of HIV-1 Rev (residues 1-93)-RNA aptamer complex Deposited 2018-02-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric	Chain F 1–93（93 aa） Fragment：UNP residues 1-93	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291.15 K；2% v/v 1,4-dioxane, 0.1 M Tris, pH 8.0, 15% w/v PEG3350	Resolution 3.00 Å R-free 0.241

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q76PP8_HV1
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–116； UniProt 1–116 Author chain D； PDBConstruct 1–116； UniProt 1–116 Author chain E； PDBConstruct 1–116； UniProt 1–116 Author chain F； PDBConstruct 1–116； UniProt 1–116

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	11bc
Deposition date deposition_date	2026-02-15
Structure title title	Human Nap1 in complex with HIV-1 Rev
Keywords keywords	histone chaperone, H2A-H2B, Nap1, HIV-1 Rev, Nucleosome assembly protein 1, Nucleosome assembly protein like 1, CHAPERONE; CHAPERONE
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	31.02 Å
Radius of gyration Rg (electron density) rg_electron	30.13 Å
Forward intensity I(0) i0	154364000.00
Molecular weight molecular_weight	96210.0 kDa
Excluded volume excluded_volume	119850 Å³
Envelope volume envelope_volume	173640 Å³
Hydration-shell volume shell_volume	46727 Å³
Envelope diameter envelope_diameter	113.7 Å
Shell Rg shell_rg	38.26 Å
Envelope Rg envelope_rg	30.14 Å
Shape Rg shape_rg	30.11 Å
Total Rg total_rg	31.00 Å
Total atoms total_atoms	6793
Residues n_residues	826
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	101.6 Å
Rg (real space) rg_real	30.85 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	1.5440e+08
I(0) uncertainty (real space) i0_real_error	2.2530e+06
Rg (reciprocal space) rg_reciprocal	30.92 Å
I(0) (reciprocal space) i0_reciprocal	154400000.0000
Solution quality estimate total_estimate	0.8775
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	39.8 Å
Skewness Skewness skewness	0.220
Kurtosis Kurtosis kurtosis	-0.262
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0003
Highest regularization parameter α highest_alpha	38630000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.811; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.973

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Nucleosome assembly protein 1-like 1
Molecular weight formula_weight	45430.0 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	6793

MADIDNKEQSELDQDLDDVEEVEEEETGEETKLKARQLTVQMMQNPQILAALQERLDGLVETPTGYIESLPRVVKRRVNALKNLQVKCAQIEAKFYEEVHDLERKYAVLYQPLFDKRFEIINAIYEPTEEECEWKPDEEDEISEELKEKAKIEDEKKDEEKEDPKGIPEFWLTVFKNVDLLSDMVQEHDEPILKHLKDIKVKFSDAGQPMSFVLEFHFEPNEYFTNEVLTKTYRMRSEPDDSDPFSFDGPEIMGCTGCQIDWKKGKNVTLKTIKKKQKHKGRGTVRTVTKTVSNDSFFNFFAPPEVPESGDLDDDAEAILAADFEIGHFLRERIIPRSVLYFTGEAIEDDDDDYDEEGEEADEEGEEEGDEENDPDYDPKKDQNPAECKQQ

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 polymer

Description description	Protein Rev
Molecular weight formula_weight	13142.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,F,E

MAGRSGDSDEDLLKTVRLIKFLYQSNPPPNPEGTRQARRNRRRRWRERRRQIHSISRRILSTYLGRSAEPVPLQLPPLERLTLDCNEDCGTSGTQGVGSPQILVESPTVLESGAKE

来源 Source

来源生物 organism	Human immunodeficiency virus 1
NCBI Class编号 ncbi_taxonomy_id	11676
宿主生物 host_organism	Escherichia coli

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

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

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.30 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	275000

fit	/app/data/saxs_computation/1b/11bc/11bc.fit
pddf	/app/data/pr_computation/1b/11bc/11bc.pr.out
profile	/app/data/saxs_computation/1b/11bc/11bc.dat

Human Nap1 in complex with HIV-1 Rev

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

Nucleosome assembly protein 1-like 1

State in the Current Structure

Other States of the Same Protein in the Database

Protein Rev

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)