[English] 日本語
Yorodumi
- PDB-8pi2: Native alpha-1-antitrypsin at 1.5 Angstrom (Cys232Ser) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pi2
TitleNative alpha-1-antitrypsin at 1.5 Angstrom (Cys232Ser)
ComponentsAlpha-1-antitrypsin
KeywordsPROTEIN BINDING / Antitrypsin / protease inhibitor / serpin / native
Function / homology
Function and homology information


Cargo concentration in the ER / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation ...Cargo concentration in the ER / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / collagen-containing extracellular matrix / protease binding / ficolin-1-rich granule lumen / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / Neutrophil degranulation / Golgi apparatus / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Serpin, conserved site / Serpins signature. / 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
GLYCINE / Alpha-1-antitrypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsWang, M. / Irving, J.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V034243/1 United Kingdom
Other privateAlpha-1 Foundation to JI
CitationJournal: To Be Published
Title: Structural determinants of instability in alpha-1-antitrypsin
Authors: Aldobiyan, I. / Wang, M. / Irving, J.A. / Lomas, D.A.
History
DepositionJun 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-1-antitrypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8114
Polymers45,5961
Non-polymers2153
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.566, 38.994, 89.247
Angle α, β, γ (deg.)90.000, 103.880, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein Alpha-1-antitrypsin / Alpha-1 protease inhibitor / Alpha-1-antiproteinase / Serpin A1


Mass: 45595.680 Da / Num. of mol.: 1 / Mutation: C232S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA1, AAT, PI, PRO0684, PRO2209 / Organ: Liver / Plasmid: pQE-31 / Details (production host): T5 / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): XL-1 Blue / References: UniProt: P01009
#2: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.8 % / Description: Plate
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.75 / Details: 0.1M malonate-imidazole-borate pH5.75, 25% PEG1500

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 8, 2020
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.48→86.64 Å / Num. obs: 63873 / % possible obs: 99.5 % / Redundancy: 3.2 % / Biso Wilson estimate: 21.37 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.06 / Rrim(I) all: 0.109 / Χ2: 0.43 / Net I/σ(I): 5.4
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.414 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3170 / CC1/2: 0.297 / Rpim(I) all: 0.923 / Rrim(I) all: 1.695 / Χ2: 0.42 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.4data scaling
autoPROC1.0.5data processing
XDS20200417data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→55.61 Å / SU ML: 0.2376 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.1117
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1948 1996 3.13 %
Rwork0.1685 61718 -
obs0.1693 63714 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.98 Å2
Refinement stepCycle: LAST / Resolution: 1.48→55.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2828 0 13 325 3166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00393000
X-RAY DIFFRACTIONf_angle_d0.73174092
X-RAY DIFFRACTIONf_chiral_restr0.0642485
X-RAY DIFFRACTIONf_plane_restr0.0064524
X-RAY DIFFRACTIONf_dihedral_angle_d16.81861094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.520.41261400.36494334X-RAY DIFFRACTION98.35
1.52-1.560.36331420.31124392X-RAY DIFFRACTION99.21
1.56-1.60.28661420.25534365X-RAY DIFFRACTION99.01
1.6-1.660.28891410.22544368X-RAY DIFFRACTION99.6
1.66-1.710.25071440.2044426X-RAY DIFFRACTION99.43
1.71-1.780.25441410.19874412X-RAY DIFFRACTION99.76
1.78-1.860.26991430.19734400X-RAY DIFFRACTION99.56
1.86-1.960.21541430.18184397X-RAY DIFFRACTION99.63
1.96-2.090.20861430.14664450X-RAY DIFFRACTION99.83
2.09-2.250.18821430.14084411X-RAY DIFFRACTION99.67
2.25-2.470.18961430.1474436X-RAY DIFFRACTION99.52
2.47-2.830.17921430.15534440X-RAY DIFFRACTION98.94
2.83-3.570.18781430.16034427X-RAY DIFFRACTION98.2
3.57-55.610.14811450.1574460X-RAY DIFFRACTION96.68

+
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://pdbjlvh1.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