[English] 日本語
Yorodumi
- PDB-9ih0: Crystal structure of Vaspin with PolyP45 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ih0
TitleCrystal structure of Vaspin with PolyP45
ComponentsSerpin A12
KeywordsPROTEIN BINDING / DNA / serpin / polyphosphate / adipocytes / translocation
Function / homology
Function and homology information


regulation of triglyceride metabolic process / negative regulation of lipid biosynthetic process / regulation of cholesterol metabolic process / molecular function inhibitor activity / lipid biosynthetic process / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / gluconeogenesis / phosphatidylinositol 3-kinase/protein kinase B signal transduction / serine-type endopeptidase inhibitor activity ...regulation of triglyceride metabolic process / negative regulation of lipid biosynthetic process / regulation of cholesterol metabolic process / molecular function inhibitor activity / lipid biosynthetic process / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / gluconeogenesis / phosphatidylinositol 3-kinase/protein kinase B signal transduction / serine-type endopeptidase inhibitor activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / extracellular space / plasma membrane
Similarity search - Function
Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsUseini, A. / Strater, N. / Heiker, J.T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)209933838 Germany
CitationJournal: Febs J. / Year: 2025
Title: Vaspin identified as a DNA-binding serpin with functional consequences for protease inhibition.
Authors: Mohlis, K. / Useini, A. / Betat, H. / Bonin, S. / Broghammer, H. / Nuwayhid, R. / Langer, S. / Morl, M. / Strater, N. / Heiker, J.T.
History
DepositionFeb 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serpin A12
B: Serpin A12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2624
Polymers95,1882
Non-polymers1,0742
Water79344
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-9 kcal/mol
Surface area32740 Å2
Unit cell
Length a, b, c (Å)143.257, 147.977, 62.464
Angle α, β, γ (deg.)90.00, 104.95, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Serpin A12 / OL-64 / Visceral adipose tissue-derived serine protease inhibitor / Vaspin / Visceral adipose-specific serpin


Mass: 47593.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IW75
#2: Chemical ChemComp-A1I43 / dodecaphosphate


Mass: 977.774 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H14O37P12 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.39 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.1 M ammonium sulfate, 0.1 M sodium citrate, pH 5.1, 9% (w/v) PEG 4000, 5% (v/v) DMSO, 0.5% (w/v) n-Octyl-beta-D-glucoside

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.26→101.08 Å / Num. obs: 40630 / % possible obs: 91.2 % / Redundancy: 7 % / CC1/2: 0.998 / Net I/σ(I): 11.4
Reflection shellResolution: 2.26→2.48 Å / Num. unique obs: 2032 / CC1/2: 0.569

-
Processing

Software
NameVersionClassification
STARANISOdata scaling
XDSdata reduction
PHASER2.8.3phasing
REFMAC5.8.0419refinement
Coot0.9.8.93model building
PHENIX1.21.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→35.37 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2404 2059 5.07 %
Rwork0.2178 --
obs0.2189 40596 69.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.26→35.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6007 0 54 44 6105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.518
X-RAY DIFFRACTIONf_dihedral_angle_d13.3152391
X-RAY DIFFRACTIONf_chiral_restr0.043921
X-RAY DIFFRACTIONf_plane_restr0.0041059
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.310.327740.477487X-RAY DIFFRACTION2
2.31-2.370.4951110.3823291X-RAY DIFFRACTION
2.37-2.430.3635400.3676761X-RAY DIFFRACTION20
2.43-2.510.3728720.32431314X-RAY DIFFRACTION35
2.51-2.590.3709990.31021816X-RAY DIFFRACTION49
2.59-2.680.3411090.30322291X-RAY DIFFRACTION62
2.68-2.790.34491550.29692826X-RAY DIFFRACTION76
2.79-2.910.31652040.29463331X-RAY DIFFRACTION91
2.91-3.070.33631880.28263705X-RAY DIFFRACTION100
3.07-3.260.3211840.28013658X-RAY DIFFRACTION98
3.26-3.510.26341820.22353641X-RAY DIFFRACTION98
3.51-3.860.21662060.19623706X-RAY DIFFRACTION100
3.86-4.420.21632120.17553718X-RAY DIFFRACTION100
4.42-5.570.17962020.16913702X-RAY DIFFRACTION100
5.57-35.370.20761910.21273690X-RAY DIFFRACTION97

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more