SAXSdb — 7c7x

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

Histone H2A.6

Arabidopsis thaliana

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 14–106 Chain C； UniProt 14–106	Not recorded	Histone H2B.1 × 2 （Q9LQQ4） NAP1-related protein 1 × 2 （Q9CA59） GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；1 M NaCl, 0.1 M sodium cacodylate, 30% (v/v) PEG 600, 10% (v/v) glycerol	Resolution 3.00 Å R-free 0.262

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 7C7X	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7BP2 Structural mechanism directing nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1) Deposited 2020-03-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 14–106（93 aa）	Not recorded	SO4 SULFATE ION × 5 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.2M Sodium sulphate 0.1M Bis Tris propane pH 7.5 20% w/v PEG 3350	Resolution 1.58 Å R-free 0.186
7BP2 Structural mechanism directing nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1) Deposited 2020-03-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 14–106（93 aa）	Not recorded	SO4 SULFATE ION × 5 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.2M Sodium sulphate 0.1M Bis Tris propane pH 7.5 20% w/v PEG 3350	Resolution 1.58 Å R-free 0.186
7BP4 Structural insights into nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1) Deposited 2020-03-21	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 G 14–106（93 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；290 K；0.7 M ammonium dihydrogen phosphate, 0.07 M sodium citrate and 30% (v/v) glycerol (pH 5.6)	Resolution 2.10 Å R-free 0.226
7BP4 Structural insights into nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1) Deposited 2020-03-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 14–106（93 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；290 K；0.7 M ammonium dihydrogen phosphate, 0.07 M sodium citrate and 30% (v/v) glycerol (pH 5.6)	Resolution 2.10 Å R-free 0.226
7BP5 Structural insights into nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1) Deposited 2020-03-21	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 14–106（93 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；0.2 M sodium acetate, 20% PEG 3350	Resolution 1.90 Å R-free 0.216
7BP6 Structural insights into nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1) Deposited 2020-03-21	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 C 14–106（93 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；0.2 M sodium nitrate, 0.1 M Bis-Tris propane and 20% (w/v) PEG 3350 (pH 8.5)	Resolution 1.58 Å R-free 0.200
8KCB Complex of DDM1-nucleosome(H2A) complex with DDM1 bound to SHL2 Deposited 2023-08-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain A 1–130（130 aa） Chain B 1–130（130 aa）	Not recorded	BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.17 Å
8WH5 Structure of DDM1-nucleosome complex in the apo state Deposited 2023-09-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain C 1–130（130 aa） Chain G 1–130（130 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.58 Å
8WH8 Structure of DDM1-nucleosome complex in ADP state Deposited 2023-09-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain C 1–130（130 aa） Chain G 1–130（130 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
8WH9 Structure of DDM1-nucleosome complex in ADP-BeFx state Deposited 2023-09-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain C 1–130（130 aa） Chain G 1–130（130 aa）	Not recorded	BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.31 Å
8WHA Structure of DDM1-nucleosome complex in the ADP-BeFx state with DDM1 bound to SHL2 and SHL-2 Deposited 2023-09-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain C 1–130（130 aa） Chain G 1–130（130 aa）	Not recorded	BEF BERYLLIUM TRIFLUORIDE ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.05 Å
8WHB Structure of nucleosome core particle of Arabidopsis thaliana Deposited 2023-09-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain C 1–130（130 aa） Chain G 1–130（130 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.17 Å
9K40 Cryo-EM structure of Arabidopsis thaliana H2A-nucleosome with Arabidopsis native 147bp DNA 15.2.2 (C2 symmetry) Deposited 2024-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain C 1–130（130 aa） Chain G 1–130（130 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
9K42 Cryo-EM structure of Arabidopsis thaliana H2A-nucleosome with 147bp Widom 601 DNA (C2 symmetry) Deposited 2024-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain C 1–130（130 aa） Chain G 1–130（130 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.14 Å
9K44 Cryo-EM structure of Arabidopsis thaliana H2A-H3.3-nucleosome with Arabidopsis native 147bp DNA 15.2.2 (C2 symmetry) Deposited 2024-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain C 1–130（130 aa） Chain G 1–130（130 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.22 Å

13 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	H2A6_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–93； UniProt 14–106 Author chain C； PDBConstruct 1–93； UniProt 14–106

Histone H2B.1

Arabidopsis thaliana

UniProt Q9LQQ4

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 B； UniProt 51–148 Chain D； UniProt 51–148	Not recorded	Histone H2A.6 × 2 （Q9LD28） NAP1-related protein 1 × 2 （Q9CA59） GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；1 M NaCl, 0.1 M sodium cacodylate, 30% (v/v) PEG 600, 10% (v/v) glycerol	Resolution 3.00 Å R-free 0.262

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 7C7X	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6M2M A role for histone chaperone OsChz1 in histone recognition and deposition Deposited 2020-02-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain B 51–148（98 aa） Chain D 51–148（98 aa） Chain F 51–148（98 aa） Chain H 51–148（98 aa） Chain J 51–148（98 aa） Chain L 51–148（98 aa）	Not recorded	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.2M Sodium citrate,0.1M Tris-HCl pH 8.5, 30%(w/v)	Resolution 2.85 Å R-free 0.253
7BP2 Structural mechanism directing nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1) Deposited 2020-03-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 51–148（98 aa）	Not recorded	SO4 SULFATE ION × 5 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.2M Sodium sulphate 0.1M Bis Tris propane pH 7.5 20% w/v PEG 3350	Resolution 1.58 Å R-free 0.186
7BP2 Structural mechanism directing nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1) Deposited 2020-03-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 51–148（98 aa）	Not recorded	SO4 SULFATE ION × 5 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.2M Sodium sulphate 0.1M Bis Tris propane pH 7.5 20% w/v PEG 3350	Resolution 1.58 Å R-free 0.186
7BP4 Structural insights into nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1) Deposited 2020-03-21	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 H 51–148（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；290 K；0.7 M ammonium dihydrogen phosphate, 0.07 M sodium citrate and 30% (v/v) glycerol (pH 5.6)	Resolution 2.10 Å R-free 0.226
7BP4 Structural insights into nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1) Deposited 2020-03-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 51–148（98 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；290 K；0.7 M ammonium dihydrogen phosphate, 0.07 M sodium citrate and 30% (v/v) glycerol (pH 5.6)	Resolution 2.10 Å R-free 0.226
7BP5 Structural insights into nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1) Deposited 2020-03-21	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 B 51–148（98 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；0.2 M sodium acetate, 20% PEG 3350	Resolution 1.90 Å R-free 0.216
7BP6 Structural insights into nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1) Deposited 2020-03-21	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 D 51–148（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；0.2 M sodium nitrate, 0.1 M Bis-Tris propane and 20% (w/v) PEG 3350 (pH 8.5)	Resolution 1.58 Å R-free 0.200
9K3Z Cryo-EM structure of Arabidopsis thaliana H2A.Z-nucleosome with Arabidopsis native 147bp DNA 15.2.2 (C2 symmetry) Deposited 2024-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain D 1–148（148 aa） Chain H 1–148（148 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.75 Å
9K40 Cryo-EM structure of Arabidopsis thaliana H2A-nucleosome with Arabidopsis native 147bp DNA 15.2.2 (C2 symmetry) Deposited 2024-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain D 1–148（148 aa） Chain H 1–148（148 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
9K41 Cryo-EM structure of Arabidopsis thaliana H2A.W-nucleosome with Arabidopsis native 147bp DNA 15.2.2 (C2 symmetry) Deposited 2024-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain D 1–148（148 aa） Chain H 1–148（148 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.81 Å
9K42 Cryo-EM structure of Arabidopsis thaliana H2A-nucleosome with 147bp Widom 601 DNA (C2 symmetry) Deposited 2024-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain D 1–148（148 aa） Chain H 1–148（148 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.14 Å
9K43 Cryo-EM structure of Arabidopsis thaliana H2A.Z-nucleosome with 147bp Widom 601 DNA (C2 symmetry) Deposited 2024-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain D 1–148（148 aa） Chain H 1–148（148 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.87 Å
9K44 Cryo-EM structure of Arabidopsis thaliana H2A-H3.3-nucleosome with Arabidopsis native 147bp DNA 15.2.2 (C2 symmetry) Deposited 2024-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain D 1–148（148 aa） Chain H 1–148（148 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.22 Å
9K45 Cryo-EM structure of Arabidopsis thaliana H2A.Z-H3.3-nucleosome with Arabidopsis native 147bp DNA 15.2.2 (C2 symmetry) Deposited 2024-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain D 1–148（148 aa） Chain H 1–148（148 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.71 Å
9K46 Cryo-EM structure of Arabidopsis thaliana H2A.W-H3.3-nucleosome with Arabidopsis native 147bp DNA 15.2.2 (C2 symmetry) Deposited 2024-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain D 1–148（148 aa） Chain H 1–148（148 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.85 Å

13 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	H2B1_ARATH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–98； UniProt 51–148 Author chain D； PDBConstruct 1–98； UniProt 51–148

NAP1-related protein 1

Arabidopsis thaliana

UniProt Q9CA59

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 E； UniProt 19–256 Chain F； UniProt 19–256	Not recorded	Histone H2A.6 × 2 （Q9LD28） Histone H2B.1 × 2 （Q9LQQ4） GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；1 M NaCl, 0.1 M sodium cacodylate, 30% (v/v) PEG 600, 10% (v/v) glycerol	Resolution 3.00 Å R-free 0.262

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 7C7X	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5DAY The structure of NAP1-Related Protein(NRP1) in Arabidopsis Deposited 2015-08-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 19–225（207 aa） Fragment：UNP RESIDUES 19-225 Chain B 19–225（207 aa） Fragment：UNP RESIDUES 19-225	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；289.15 K；25% PEG 400, 0.1 M HEPES pH 7.6, 0.2 M Calcium chloride dihydrate	Resolution 2.33 Å R-free 0.269
7BP6 Structural insights into nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1) Deposited 2020-03-21	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 226–232（7 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；0.2 M sodium nitrate, 0.1 M Bis-Tris propane and 20% (w/v) PEG 3350 (pH 8.5)	Resolution 1.58 Å R-free 0.200

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NRP1_ARATH
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 2–239； UniProt 19–256 Author chain F； PDBConstruct 2–239； UniProt 19–256

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	7c7x
Deposition date deposition_date	2020-05-27
Structure title title	Structural insights into nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1)
Keywords keywords	complex, Histone, PLANT PROTEIN, CHAPERONE, TRANSCRIPTION-CHAPERONE complex; TRANSCRIPTION/CHAPERONE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	34.65 Å
Radius of gyration Rg (electron density) rg_electron	34.36 Å
Forward intensity I(0) i0	87302500.00
Molecular weight molecular_weight	77493.0 kDa
Excluded volume excluded_volume	98632 Å³
Envelope volume envelope_volume	143040 Å³
Hydration-shell volume shell_volume	36682 Å³
Envelope diameter envelope_diameter	129.2 Å
Shell Rg shell_rg	38.78 Å
Envelope Rg envelope_rg	33.33 Å
Shape Rg shape_rg	34.33 Å
Total Rg total_rg	34.87 Å
Total atoms total_atoms	5478
Residues n_residues	683
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	117.8 Å
Rg (real space) rg_real	34.70 Å
Rg uncertainty (real space) rg_real_error	1.11 Å
I(0) (real space) i0_real	8.7300e+07
I(0) uncertainty (real space) i0_real_error	1.4630e+06
Rg (reciprocal space) rg_reciprocal	34.67 Å
I(0) (reciprocal space) i0_reciprocal	87300000.0000
Solution quality estimate total_estimate	0.6556
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	43.5 Å
Skewness Skewness skewness	0.364
Kurtosis Kurtosis kurtosis	-0.228
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13330000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.868; Stabil: 1.000; Sysdev: 0.038; Positv: 1.000; Valcen: 0.984; Smooth: 0.817

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Histone H2A.6
Molecular weight formula_weight	10033.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,A
Atom count atom_count	5502

KKATSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKTRIVPRHIQLAVRNDEELSKLLGDVTIAN

来源 Source

来源生物 organism	Arabidopsis thaliana
通用名 common_name	Mouse-ear cress
NCBI Class编号 ncbi_taxonomy_id	3702
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Histone H2B.1
Molecular weight formula_weight	11033.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,B

KKRSKKNVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSKLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS

来源 Source

来源生物 organism	Arabidopsis thaliana
通用名 common_name	Mouse-ear cress
NCBI Class编号 ncbi_taxonomy_id	3702
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	NAP1-related protein 1
Molecular weight formula_weight	27484.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SNLEQIDAELVLSIEKLQEIQDDLEKINEKASDEVLEVEQKYNVIRKPVYDKRNEVIQSIPGFWMTAFLSHPALGDLLTEEDQKIFKYLNSLEVEDAKDVKSGYSITFHFTSNPFFEDAKLTKTFTFLEEGTTKITATPIKWKEGKGLPNGVNHDDKKGNKRALPEESFFTWFTDAQHKEDAGDEIHDEVADIIKEDLWSNPLTYFNNDADEEDFDGDDDGDEEGEEDDDDEEEEDGEE

来源 Source

来源生物 organism	Arabidopsis thaliana
通用名 common_name	Mouse-ear cress
NCBI Class编号 ncbi_taxonomy_id	3702
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	24

▼

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d7c7xa_
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.1 — Nucleosome core histones

Domain ID domain_id	d7c7xb_
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.1 — Nucleosome core histones

Domain ID domain_id	d7c7xc_
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.1 — Nucleosome core histones

Domain ID domain_id	d7c7xd_
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.1 — Nucleosome core histones

Domain ID domain_id	d7c7xe1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.305 — NAP-like
Superfamily Superfamily superfamily	d.305.1 — NAP-like
Family Family family	d.305.1.0 — automated matches

Domain ID domain_id	d7c7xe2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d7c7xf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.305 — NAP-like
Superfamily Superfamily superfamily	d.305.1 — NAP-like
Family Family family	d.305.1.0 — automated matches

▶

8. Citations (1)

▶

Unit-cell length a length_a	66.710 Å
Unit-cell length b length_b	128.396 Å
Unit-cell length c length_c	140.275 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	29.620 Å
R factor r_factor	0.2248
R_work r_work	0.2229
R_free r_free	0.2617

fit	/app/data/saxs_computation/c7/7c7x/7c7x.fit
pddf	/app/data/pr_computation/c7/7c7x/7c7x.pr.out
profile	/app/data/saxs_computation/c7/7c7x/7c7x.dat

Structural insights into nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1)

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

Histone H2A.6

State in the Current Structure

Other States of the Same Protein in the Database

Histone H2B.1

State in the Current Structure

Other States of the Same Protein in the Database

NAP1-related protein 1

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

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (7 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)