[English] 日本語
Yorodumi
- PDB-3r2p: 2.2 Angstrom Crystal Structure of C Terminal Truncated Human Apol... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3r2p
Title2.2 Angstrom Crystal Structure of C Terminal Truncated Human Apolipoprotein A-I Reveals the Assembly of HDL by Dimerization.
ComponentsApolipoprotein A-I
KeywordsLIPID TRANSPORT / amphipathic alpha-helix / major protein of high density lipoprotein (HDL) / lipid binding / plasma
Function / homology
Function and homology information


Defective ABCA1 causes TGD / high-density lipoprotein particle receptor binding / peptidyl-methionine modification / HDL clearance / spherical high-density lipoprotein particle / Scavenging by Class B Receptors / negative regulation of response to cytokine stimulus / protein oxidation / regulation of intestinal cholesterol absorption / vitamin transport ...Defective ABCA1 causes TGD / high-density lipoprotein particle receptor binding / peptidyl-methionine modification / HDL clearance / spherical high-density lipoprotein particle / Scavenging by Class B Receptors / negative regulation of response to cytokine stimulus / protein oxidation / regulation of intestinal cholesterol absorption / vitamin transport / blood vessel endothelial cell migration / cholesterol import / negative regulation of heterotypic cell-cell adhesion / high-density lipoprotein particle binding / ABC transporters in lipid homeostasis / apolipoprotein A-I receptor binding / apolipoprotein receptor binding / negative regulation of cell adhesion molecule production / negative regulation of cytokine production involved in immune response / HDL assembly / negative regulation of very-low-density lipoprotein particle remodeling / phosphatidylcholine biosynthetic process / glucocorticoid metabolic process / acylglycerol homeostasis / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / Chylomicron remodeling / cellular response to lipoprotein particle stimulus / Chylomicron assembly / high-density lipoprotein particle clearance / phospholipid efflux / chylomicron / high-density lipoprotein particle remodeling / positive regulation of cholesterol metabolic process / lipid storage / reverse cholesterol transport / phospholipid homeostasis / high-density lipoprotein particle assembly / chemorepellent activity / low-density lipoprotein particle / lipoprotein biosynthetic process / cholesterol transfer activity / cholesterol transport / high-density lipoprotein particle / very-low-density lipoprotein particle / endothelial cell proliferation / regulation of Cdc42 protein signal transduction / HDL remodeling / cholesterol efflux / Scavenging by Class A Receptors / triglyceride homeostasis / adrenal gland development / negative chemotaxis / negative regulation of interleukin-1 beta production / cholesterol binding / cholesterol biosynthetic process / amyloid-beta formation / positive regulation of Rho protein signal transduction / positive regulation of cholesterol efflux / endocytic vesicle / negative regulation of tumor necrosis factor-mediated signaling pathway / Scavenging of heme from plasma / Retinoid metabolism and transport / cholesterol metabolic process / positive regulation of stress fiber assembly / heat shock protein binding / endocytic vesicle lumen / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of phagocytosis / cholesterol homeostasis / integrin-mediated signaling pathway / Post-translational protein phosphorylation / Heme signaling / PPARA activates gene expression / phospholipid binding / negative regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Platelet degranulation / extracellular vesicle / : / amyloid-beta binding / cytoplasmic vesicle / blood microparticle / secretory granule lumen / early endosome / protein stabilization / G protein-coupled receptor signaling pathway / Amyloid fiber formation / receptor ligand activity / endoplasmic reticulum lumen / signaling receptor binding / enzyme binding / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #20 / Apolipoprotein / Apolipoprotein A/E / : / Apolipoprotein A1/A4/E domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2045 Å
AuthorsMei, X. / Atkinson, D.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal Structure of C-terminal Truncated Apolipoprotein A-I Reveals the Assembly of High Density Lipoprotein (HDL) by Dimerization.
Authors: Mei, X. / Atkinson, D.
History
DepositionMar 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references / Structure summary
Revision 1.2Nov 16, 2011Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Apolipoprotein A-I


Theoretical massNumber of molelcules
Total (without water)21,6561
Polymers21,6561
Non-polymers00
Water68538
1
A: Apolipoprotein A-I

A: Apolipoprotein A-I


Theoretical massNumber of molelcules
Total (without water)43,3122
Polymers43,3122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area7850 Å2
ΔGint-74 kcal/mol
Surface area21820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.333, 30.178, 69.576
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operations: -x, -y, z and x, y+1, Z

-
Components

#1: Protein Apolipoprotein A-I / Apo-AI / ApoA-I / Apolipoprotein A1 / Apolipoprotein A-I(1-242)


Mass: 21656.234 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP 25-208)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOA1 / Plasmid: pDEST-His6-MBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus-RIL / References: UniProt: P02647
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.15M potassium bromide, 30% PEG 2000 MME, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.91994 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 15, 2010
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91994 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 11930 / Num. obs: 11930 / % possible obs: 98.2 % / Observed criterion σ(F): 2.95 / Observed criterion σ(I): 2.95 / Redundancy: 6.4 % / Biso Wilson estimate: 37.46 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 21.017
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.95 / Num. unique all: 532 / % possible all: 89.4

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIX(phenix.autoMR: 1.6.2_432)model building
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.6.2_432phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Use the Se-Met derivative to obtain the starting model from SAD experiment.

Resolution: 2.2045→34.788 Å / SU ML: 0.33 / Isotropic thermal model: Mixed individual ADP with TLS / σ(F): 0 / Phase error: 33.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1191 10 %Random
Rwork0.2304 ---
all0.2356 11905 --
obs0.2356 11905 97.94 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.738 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso mean: 63.7952 Å2
Baniso -1Baniso -2Baniso -3
1-29.7755 Å2-0 Å2-0 Å2
2---7.8408 Å2-0 Å2
3----21.9347 Å2
Refinement stepCycle: LAST / Resolution: 2.2045→34.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1485 0 0 38 1523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071512
X-RAY DIFFRACTIONf_angle_d0.9582036
X-RAY DIFFRACTIONf_dihedral_angle_d15.182597
X-RAY DIFFRACTIONf_chiral_restr0.063216
X-RAY DIFFRACTIONf_plane_restr0.006268
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.2045-2.29280.40771190.31741071119090
2.2928-2.39710.33271250.31471129125496
2.3971-2.52350.38971340.29491198133299
2.5235-2.68150.40391300.28221174130499
2.6815-2.88850.36941320.257611911323100
2.8885-3.1790.30031350.264512131348100
3.179-3.63850.29661350.226512101345100
3.6385-4.58250.24651370.185812361373100
4.5825-34.79230.21151440.20571292143697
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)
11.09831.2873-0.0630.40770.61411.0623-0.0298-0.1037-0.0480.1332-0.0261-0.04680.0586-0.02790.01560.39220.0567-0.03710.23070.00120.3004-29.3098-6.66-29.4704
21.39920.84190.5310.60241.25971.23720.001-0.51060.4050.2537-0.34120.1984-0.1468-0.50150.22680.44030.1640.03760.3768-0.02080.3744-35.02730.8897-16.3313
32.77261.80270.79991.27860.81842.6795-0.06220.91020.5465-0.41710.21060.62020.4491-0.1734-0.12980.68320.0308-0.02340.5182-0.06040.7208-0.963121.79865.4763
42.43881.5867-1.94511.1174-1.14171.70780.4472-0.49860.3120.54950.00460.149-0.28880.4394-0.18970.44050.0356-0.04570.3234-0.00760.320732.551639.7184-18.7399
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 4:76)
2X-RAY DIFFRACTION2(chain A and resid 77:119)
3X-RAY DIFFRACTION3(chain A and resid 120:144)
4X-RAY DIFFRACTION4(chain A and resid 145:183)

+
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