[English] 日本語
Yorodumi
- PDB-5u6g: Crystal Structure of the holo Domain-Swapped Dimer mutant Q108K:K... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5u6g
TitleCrystal Structure of the holo Domain-Swapped Dimer mutant Q108K:K40D Human Cellular Retinol Binding Protein II bound with all trans retinal
Components(Retinol-binding protein 2) x 2
KeywordsTRANSPORT PROTEIN / Domain Swapped Dimer / Domain Swapping / Protein folding / Intra Cellular / all trans retinal
Function / homology
Function and homology information


vitamin A metabolic process / retinoid binding / retinal binding / retinol binding / epidermis development / fatty acid transport / Retinoid metabolism and transport / fatty acid binding / nucleus / cytosol
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
RETINAL / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsAssar, Z. / Geiger, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Citation
Journal: To Be Published
Title: Crystal Structure of the holo Domain-Swapped Dimer mutant Q108K:K40D Human Cellular Retinol Binding Protein II bound with all trans retinal
Authors: Assar, Z. / Geiger, J.H.
#1: Journal: Structure / Year: 2016
Title: Domain-Swapped Dimers of Intracellular Lipid-Binding Proteins: Evidence for Ordered Folding Intermediates.
Authors: Assar, Z. / Nossoni, Z. / Wang, W. / Santos, E.M. / Kramer, K. / McCornack, C. / Vasileiou, C. / Borhan, B. / Geiger, J.H.
#2: Journal: Science / Year: 2012
Title: Tuning the electronic absorption of protein-embedded all-trans-retinal.
Authors: Wang, W. / Nossoni, Z. / Berbasova, T. / Watson, C.T. / Yapici, I. / Lee, K.S. / Vasileiou, C. / Geiger, J.H. / Borhan, B.
History
DepositionDec 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Retinol-binding protein 2
B: Retinol-binding protein 2
C: Retinol-binding protein 2
D: Retinol-binding protein 2
H: Retinol-binding protein 2
E: Retinol-binding protein 2
F: Retinol-binding protein 2
G: Retinol-binding protein 2
I: Retinol-binding protein 2
J: Retinol-binding protein 2
K: Retinol-binding protein 2
L: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,17023
Polymers187,04112
Non-polymers3,12911
Water3,405189
1
A: Retinol-binding protein 2
F: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7384
Polymers31,1692
Non-polymers5692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9260 Å2
ΔGint-33 kcal/mol
Surface area12900 Å2
MethodPISA
2
B: Retinol-binding protein 2
E: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7384
Polymers31,1692
Non-polymers5692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9260 Å2
ΔGint-30 kcal/mol
Surface area12790 Å2
MethodPISA
3
C: Retinol-binding protein 2
G: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7524
Polymers31,1832
Non-polymers5692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9330 Å2
ΔGint-34 kcal/mol
Surface area12990 Å2
MethodPISA
4
D: Retinol-binding protein 2
H: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7384
Polymers31,1692
Non-polymers5692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9320 Å2
ΔGint-38 kcal/mol
Surface area12770 Å2
MethodPISA
5
I: Retinol-binding protein 2
K: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7524
Polymers31,1832
Non-polymers5692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9310 Å2
ΔGint-34 kcal/mol
Surface area12910 Å2
MethodPISA
6
J: Retinol-binding protein 2
L: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4533
Polymers31,1692
Non-polymers2841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8370 Å2
ΔGint-34 kcal/mol
Surface area13320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.474, 73.597, 351.601
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Retinol-binding protein 2 / Cellular retinol-binding protein II / CRBP-II


Mass: 15584.411 Da / Num. of mol.: 10 / Mutation: Q108K, K40D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Production host: Bacteria (eubacteria) / Strain (production host): DE3 / References: UniProt: P50120
#2: Protein Retinol-binding protein 2 / Cellular retinol-binding protein II / CRBP-II


Mass: 15598.503 Da / Num. of mol.: 2 / Mutation: Q108K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Production host: Bacteria (eubacteria) / Strain (production host): DE3 / References: UniProt: P50120
#3: Chemical
ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C20H28O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.26 Å3/Da / Density % sol: 45.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 30% PEG 4000, 0.1 M sodium acetate, 0.1 M ammonium acetate, pH 4.6

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→19.92 Å / Num. obs: 53735 / % possible obs: 99.8 % / Redundancy: 14.8 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 26.2

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PHENIXphasing
HKL-2000data scaling
PHENIXmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2rcq

2rcq


Resolution: 2.6→19 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.72
RfactorNum. reflection% reflection
Rfree0.2805 2000 3.74 %
Rwork0.1766 --
obs0.1805 53462 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13130 0 220 189 13539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01513603
X-RAY DIFFRACTIONf_angle_d1.24418355
X-RAY DIFFRACTIONf_dihedral_angle_d17.7125053
X-RAY DIFFRACTIONf_chiral_restr0.0441944
X-RAY DIFFRACTIONf_plane_restr0.0052419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5966-2.66140.38861360.24493504X-RAY DIFFRACTION97
2.6614-2.73320.36131430.24133682X-RAY DIFFRACTION100
2.7332-2.81340.35971400.2333580X-RAY DIFFRACTION100
2.8134-2.90390.30471400.2253615X-RAY DIFFRACTION100
2.9039-3.00740.30761410.2153643X-RAY DIFFRACTION100
3.0074-3.12740.30331420.20333656X-RAY DIFFRACTION100
3.1274-3.26910.31951420.19863654X-RAY DIFFRACTION100
3.2691-3.44060.2871420.18463661X-RAY DIFFRACTION100
3.4406-3.65490.30111430.17053677X-RAY DIFFRACTION100
3.6549-3.93520.24271430.1663659X-RAY DIFFRACTION100
3.9352-4.32750.23971440.14863719X-RAY DIFFRACTION100
4.3275-4.94530.22531450.13563719X-RAY DIFFRACTION100
4.9453-6.19930.28311460.17513778X-RAY DIFFRACTION100
6.1993-19.92680.28911530.16973915X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -20.7615 Å / Origin y: 55.0204 Å / Origin z: -39.7542 Å
111213212223313233
T0.3195 Å2-0.0234 Å20.0038 Å2-0.337 Å2-0.0084 Å2--0.2921 Å2
L-0.0243 °20.015 °20.0636 °2-0.0683 °20.02 °2--0.3806 °2
S-0.0159 Å °0.0092 Å °0.0203 Å °-0.0158 Å °-0.0018 Å °0.027 Å °-0.0411 Å °-0.0077 Å °0.0168 Å °
Refinement TLS groupSelection details: all

+
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