+
Open data
-
Basic information
Entry | Database: PDB / ID: 7v1l | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of sNASP core in complex with H3 alpha3 helix peptide | ||||||
![]() |
| ||||||
![]() | CHAPERONE / histone chaperone | ||||||
Function / homology | ![]() negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin formation / inner kinetochore / oocyte maturation / nucleus organization / spermatid development / subtelomeric heterochromatin formation ...negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin formation / inner kinetochore / oocyte maturation / nucleus organization / spermatid development / subtelomeric heterochromatin formation / single fertilization / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / nucleosomal DNA binding / Inhibition of DNA recombination at telomere / telomere organization / RNA Polymerase I Promoter Opening / embryo implantation / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / PRC2 methylates histones and DNA / Defective pyroptosis / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / multicellular organism growth / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / osteoblast differentiation / structural constituent of chromatin / male gonad development / nucleosome / nucleosome assembly / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cell population proliferation / chromosome, telomeric region / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein-containing complex / extracellular exosome / extracellular region / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bao, H. / Huang, H. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: NASP maintains histone H3-H4 homeostasis through two distinct H3 binding modes. Authors: Bao, H. / Carraro, M. / Flury, V. / Liu, Y. / Luo, M. / Chen, L. / Groth, A. / Huang, H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 108.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 81.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 430.5 KB | Display | |
Data in XML | ![]() | 9.9 KB | Display | |
Data in CIF | ![]() | 12.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7v1kC ![]() 7v1mC ![]() 4nq0S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 28262.490 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The sequence is amino acids 30 to 340 from sp P49321-2(NASP_HUMAN Isoform 2) with a deletion of amino acids 101-159. Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: P49321-2 |
---|---|
#2: Protein/peptide | Mass: 2385.878 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: P84243 |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.36 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.4M Na-K phosphate, pH 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 15, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9766 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.849→40 Å / Num. obs: 9497 / % possible obs: 99.8 % / Redundancy: 12 % / Biso Wilson estimate: 70.52 Å2 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.045 / Rrim(I) all: 0.149 / Χ2: 0.501 / Net I/σ(I): 2.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4NQ0 Resolution: 2.849→36.742 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.45 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 172.23 Å2 / Biso mean: 72.8168 Å2 / Biso min: 38.17 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.849→36.742 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 56.5464 Å / Origin y: 71.4866 Å / Origin z: 39.3053 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|