[English] 日本語
Yorodumi
- PDB-3r69: Molecular analysis of the interaction of the HDL-receptor SR-BI w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3r69
TitleMolecular analysis of the interaction of the HDL-receptor SR-BI with the PDZ3 domain of its adaptor protein PDZK1
ComponentsNa(+)/H(+) exchange regulatory cofactor NHE-RF3, Scavenger receptor class B member 1
KeywordsSIGNALING PROTEIN / PDZ domain / Adaptor protein / SR-BI / chimera
Function / homology
Function and homology information


vitamin transmembrane transport / carotenoid transport / high-density lipoprotein particle receptor activity / Scavenging by Class B Receptors / HDL clearance / positive regulation of cholesterol storage / intestinal lipid absorption / recognition of apoptotic cell / regulation of phosphatidylcholine catabolic process / lipopolysaccharide immune receptor activity ...vitamin transmembrane transport / carotenoid transport / high-density lipoprotein particle receptor activity / Scavenging by Class B Receptors / HDL clearance / positive regulation of cholesterol storage / intestinal lipid absorption / recognition of apoptotic cell / regulation of phosphatidylcholine catabolic process / lipopolysaccharide immune receptor activity / plasma lipoprotein particle clearance / apolipoprotein A-I binding / detection of lipopolysaccharide / high-density lipoprotein particle binding / lipopolysaccharide transport / cholesterol import / scavenger receptor binding / androgen biosynthetic process / low-density lipoprotein particle clearance / high-density lipoprotein particle remodeling / blood vessel endothelial cell migration / high-density lipoprotein particle clearance / positive regulation of triglyceride biosynthetic process / adhesion of symbiont to host / reverse cholesterol transport / low-density lipoprotein particle binding / scavenger receptor activity / phagocytosis, recognition / triglyceride homeostasis / phospholipid transport / cholesterol transport / cholesterol catabolic process / regulation of phagocytosis / cholesterol efflux / endothelial cell proliferation / lipid transport / microvillus membrane / phosphatidylserine binding / apolipoprotein binding / brush border / positive regulation of protein targeting to membrane / protein-membrane adaptor activity / cholesterol homeostasis / regulation of monoatomic anion transport / PDZ domain binding / caveola / protein localization to plasma membrane / brush border membrane / lipopolysaccharide binding / amyloid-beta binding / in utero embryonic development / lysosome / apical plasma membrane / signaling receptor binding / intracellular membrane-bounded organelle / lipid binding / protein-containing complex binding / cell surface / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
CD36/scavenger receptor class B member 1 / CD36 family / CD36 family / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily ...CD36/scavenger receptor class B member 1 / CD36 family / CD36 family / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Scavenger receptor class B member 1 / Na(+)/H(+) exchange regulatory cofactor NHE-RF3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 Å
AuthorsKocher, O. / Birrane, G. / Krieger, M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Identification of the PDZ3 Domain of the Adaptor Protein PDZK1 as a Second, Physiologically Functional Binding Site for the C Terminus of the High Density Lipoprotein Receptor Scavenger Receptor Class B Type I.
Authors: Kocher, O. / Birrane, G. / Yesilaltay, A. / Shechter, S. / Pal, R. / Daniels, K. / Krieger, M.
History
DepositionMar 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Database references
Revision 1.3Jul 26, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Na(+)/H(+) exchange regulatory cofactor NHE-RF3, Scavenger receptor class B member 1
B: Na(+)/H(+) exchange regulatory cofactor NHE-RF3, Scavenger receptor class B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0183
Polymers18,8252
Non-polymers1921
Water2,414134
1
A: Na(+)/H(+) exchange regulatory cofactor NHE-RF3, Scavenger receptor class B member 1


Theoretical massNumber of molelcules
Total (without water)9,4131
Polymers9,4131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Na(+)/H(+) exchange regulatory cofactor NHE-RF3, Scavenger receptor class B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6052
Polymers9,4131
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-7 kcal/mol
Surface area10060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.638, 61.396, 64.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Na(+)/H(+) exchange regulatory cofactor NHE-RF3, Scavenger receptor class B member 1 / NHERF-3 / CFTR-associated protein of 70 kDa / Na(+)/H(+) exchanger regulatory factor 3 / Na/Pi ...NHERF-3 / CFTR-associated protein of 70 kDa / Na(+)/H(+) exchanger regulatory factor 3 / Na/Pi cotransporter C-terminal-associated protein 1 / NaPi-Cap1 / PDZ domain-containing protein 1 / Sodium-hydrogen exchanger regulatory factor 3 / SR-BI


Mass: 9412.715 Da / Num. of mol.: 2
Fragment: PDZ3 (UNP Residues 239-323), SR-BI C-terminus (UNP Residues 505-509)
Source method: isolated from a genetically manipulated source
Details: Chimera between two genes / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cap70, Nherf3, Pdzk1, Scarb1 / Plasmid: pGEX-4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q9JIL4, UniProt: Q61009
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 0.1 M citric acid pH 3.5, 25% PEG 3350, 5% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 10, 2010 / Details: mirrors
RadiationMonochromator: Si(111) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.499→50 Å / Num. all: 29138 / Num. obs: 29138 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.499→1.55 Å / % possible all: 66.4

-
Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3R68

3r68


Resolution: 1.499→23.93 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.792 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.081 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22549 1435 4.9 %RANDOM
Rwork0.20034 ---
all0.2016 27563 --
obs0.2016 27563 94.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.819 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.499→23.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1267 0 13 134 1414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221344
X-RAY DIFFRACTIONr_bond_other_d0.0020.02920
X-RAY DIFFRACTIONr_angle_refined_deg1.7182.0091820
X-RAY DIFFRACTIONr_angle_other_deg0.97432282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3165184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.832655
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09515250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.728157
X-RAY DIFFRACTIONr_chiral_restr0.1060.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211512
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02227
X-RAY DIFFRACTIONr_mcbond_it1.2231.5866
X-RAY DIFFRACTIONr_mcbond_other0.3391.5366
X-RAY DIFFRACTIONr_mcangle_it2.07621387
X-RAY DIFFRACTIONr_scbond_it3.1073478
X-RAY DIFFRACTIONr_scangle_it5.2094.5425
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 61 -
Rwork0.237 1342 -
obs--63.14 %
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)
10.2110.0659-0.04710.9876-0.74031.1715-0.04760.0396-0.04610.07320.02420.0572-0.05850.08090.02340.02670.00640.01150.0552-0.00040.058119.93525.55333.057
20.1761-0.29570.53532.6785-1.44011.7729-0.01960.03670.00940.3582-0.0367-0.0467-0.18390.08710.05630.0772-0.0049-0.00120.07010.01040.036517.25346.95521.291
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A240 - 327
2X-RAY DIFFRACTION2B239 - 327

+
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