[English] 日本語
Yorodumi
- PDB-1rlb: RETINOL BINDING PROTEIN COMPLEXED WITH TRANSTHYRETIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rlb
TitleRETINOL BINDING PROTEIN COMPLEXED WITH TRANSTHYRETIN
Components
  • RETINOL BINDING PROTEINRetinol-binding protein
  • TRANSTHYRETIN
KeywordsCOMPLEX (PROTEIN/PROTEIN) / COMPLEX (PROTEIN-PROTEIN) / COMPLEX (PROTEIN-PROTEIN) complex
Function / homology
Function and homology information


Retinoid metabolism disease events / urinary bladder development / embryonic retina morphogenesis in camera-type eye / retinol transport / female genitalia morphogenesis / retinol transmembrane transporter activity / embryonic organ morphogenesis / maintenance of gastrointestinal epithelium / embryonic skeletal system development / negative regulation of cardiac muscle cell proliferation ...Retinoid metabolism disease events / urinary bladder development / embryonic retina morphogenesis in camera-type eye / retinol transport / female genitalia morphogenesis / retinol transmembrane transporter activity / embryonic organ morphogenesis / maintenance of gastrointestinal epithelium / embryonic skeletal system development / negative regulation of cardiac muscle cell proliferation / eye development / heart trabecula formation / cardiac muscle tissue development / retinal binding / retinol metabolic process / retinol binding / Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / uterus development / vagina development / positive regulation of immunoglobulin production / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / Retinoid metabolism and transport / response to retinoic acid / visual perception / gluconeogenesis / lung development / hormone activity / positive regulation of insulin secretion / azurophil granule lumen / glucose homeostasis / heart development / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Retinol binding protein/Purpurin / Lipocalin, ApoD type / Transthyretin/hydroxyisourate hydrolase domain / Lipocalin family conserved site / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase ...Retinol binding protein/Purpurin / Lipocalin, ApoD type / Transthyretin/hydroxyisourate hydrolase domain / Lipocalin family conserved site / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
RETINOIC ACID / Retinol-binding protein 4 / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 3.1 Å
AuthorsMonaco, H.L. / Rizzi, M. / Coda, A.
Citation
Journal: Science / Year: 1995
Title: Structure of a complex of two plasma proteins: transthyretin and retinol-binding protein.
Authors: Monaco, H.L. / Rizzi, M. / Coda, A.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization of the Macromolecular Complex Transthyretin Retinol Binding Protein
Authors: Monaco, H.L. / Mancia, F. / Rizzi, M. / Coda, A.
History
DepositionFeb 20, 1995-
Revision 1.0Apr 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRANSTHYRETIN
B: TRANSTHYRETIN
C: TRANSTHYRETIN
D: TRANSTHYRETIN
E: RETINOL BINDING PROTEIN
F: RETINOL BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,8658
Polymers95,2656
Non-polymers6012
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10560 Å2
ΔGint-60 kcal/mol
Surface area37090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)222.400, 163.400, 55.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein
TRANSTHYRETIN / / PREALBUMIN


Mass: 13776.376 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: PLASMA / References: UniProt: P02766
#2: Protein RETINOL BINDING PROTEIN / Retinol-binding protein


Mass: 20079.545 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Organ: PLASMA / References: UniProt: P02753
#3: Chemical ChemComp-REA / RETINOIC ACID / Retinoic acid


Mass: 300.435 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.5 %
Crystal
*PLUS
Density % sol: 53.5 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115-20 mg/mlprotein11
20.1 Msuccinate12
33 %ethylene glycol12
42.3 Mammonium sulfate12

-
Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 17465 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.09
Reflection
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 6 Å / Num. measured all: 47491 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 3.3 Å / % possible obs: 83.2 % / Num. unique obs: 2359

-
Processing

Software
NameClassification
MSCdata collection
X-PLORmodel building
X-PLORrefinement
MSCdata reduction
X-PLORphasing
RefinementResolution: 3.1→6 Å / σ(F): 0
Details: THERE IS CLOSE CONTACT BETWEEN RESIDUE GLU D 66 AND A SYMMETRY-RELATED COPY OF ITSELF.
RfactorNum. reflection% reflection
Rwork0.215 --
obs0.215 14891 93.5 %
Refinement stepCycle: LAST / Resolution: 3.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6582 0 42 0 6624
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_dihedral_angle_deg / Dev ideal: 26.7

+
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