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- PDB-9ln8: Structure of NAP1 in complex with H2A.Z-H2B -

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Basic information

Entry
Database: PDB / ID: 9ln8
TitleStructure of NAP1 in complex with H2A.Z-H2B
Components
  • H2A.Z-H2B
  • Nucleosome assembly protein 1-like 1
KeywordsCHAPERONE / NAP1 / H2A-H2B / H3-H4 / histone chaperone / nucleosome / H2A.Z
Function / homology
Function and homology information


cholesterol binding / double-strand break repair via homologous recombination / nucleosome assembly / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / chromatin binding / chromatin / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP)
Similarity search - Domain/homology
Nucleosome assembly protein 1-like 1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLi, X. / Li, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of NAP1 in complex with H2A.Z-H2B
Authors: Li, X.
History
DepositionJan 21, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleosome assembly protein 1-like 1
B: Nucleosome assembly protein 1-like 1
D: H2A.Z-H2B


Theoretical massNumber of molelcules
Total (without water)92,4593
Polymers92,4593
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.852, 79.257, 175.112
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nucleosome assembly protein 1-like 1


Mass: 34989.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: nap-1, CELE_D2096.8, D2096.8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q19007
#2: Protein H2A.Z-H2B


Mass: 22481.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Production host: Escherichia coli (E. coli)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 23307 / % possible obs: 98.1 % / Redundancy: 6.6 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.043 / Rrim(I) all: 0.116 / Χ2: 0.967 / Net I/σ(I): 5.9 / Num. measured all: 154407
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.8-2.855.80.64210810.7620.930.2790.7030.86195.1
2.85-2.96.50.56711780.810.9460.2320.6160.86899.7
2.9-2.966.50.50311610.8240.9510.2050.5460.89999.2
2.96-3.026.60.46111440.8660.9630.1870.4990.90699.6
3.02-3.086.40.40211620.8820.9680.1650.4360.93499
3.08-3.156.50.35411560.9040.9750.1440.3840.9899.6
3.15-3.236.40.28411710.9390.9840.1160.3080.99899.4
3.23-3.326.50.20911620.9730.9930.0840.2261.06999.3
3.32-3.426.50.20311450.9680.9920.0820.221.05499.2
3.42-3.536.30.16911760.9820.9960.0680.1831.15798.9
3.53-3.6560.14211170.9810.9950.060.1551.12896.1
3.65-3.86.30.12111460.9880.9970.050.1321.17196.6
3.8-3.976.90.1111890.990.9970.0430.1191.16399.4
3.97-4.186.90.09511790.9930.9980.0370.1021.1599.1
4.18-4.4470.08911710.9930.9980.0350.0961.11999.3
4.44-4.797.10.07911890.9930.9980.030.0851.03999
4.79-5.2770.06911540.9960.9990.0260.0740.85197.1
5.27-6.0370.0711770.9960.9990.0270.0750.76196
6.03-7.597.40.05712050.9970.9990.0220.0620.67298
7.59-506.80.04512440.9980.9990.0180.0490.64293.9

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6K0C

6k0c


Resolution: 2.8→49.06 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2581 1139 4.97 %
Rwork0.2106 --
obs0.213 22923 96.48 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→49.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5691 0 0 0 5691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065800
X-RAY DIFFRACTIONf_angle_d0.9797835
X-RAY DIFFRACTIONf_dihedral_angle_d5.694759
X-RAY DIFFRACTIONf_chiral_restr0.047883
X-RAY DIFFRACTIONf_plane_restr0.0091014
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.920.38111340.30262374X-RAY DIFFRACTION86
2.92-3.080.33771500.26262673X-RAY DIFFRACTION97
3.08-3.270.30861430.24072758X-RAY DIFFRACTION99
3.27-3.520.30821480.24272774X-RAY DIFFRACTION99
3.52-3.880.24581270.19822729X-RAY DIFFRACTION97
3.88-4.440.23731670.17892791X-RAY DIFFRACTION99
4.44-5.590.2041260.18122785X-RAY DIFFRACTION97
5.59-49.060.21441440.20062900X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0637-0.32810.30021.51160.17560.40490.0478-0.0333-0.05140.0672-0.04480.17640.02970.019-0.00290.2078-0.04180.00130.1920.00760.25336.8141-20.2203-31.2244
20.1396-0.4545-0.02331.48910.2670.4977-0.009-0.10260.04670.1803-0.0316-0.1032-0.10340.01210.0510.285-0.047-0.0470.2290.00770.22077.726.8512-25.9915
31.42350.4919-1.17331.1886-0.421.9467-0.2111-0.423-0.00470.02810.05870.14590.17370.10670.11330.31830.0498-0.00340.69970.03010.339128.695-20.3531-7.8919
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 7 through 296)
2X-RAY DIFFRACTION2(chain 'B' and resid 6 through 293)
3X-RAY DIFFRACTION3(chain 'D' and resid 31 through 212)

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