[English] 日本語
Yorodumi
- PDB-6qba: Crystal Structure of Retinol-Binding Protein 4 (RBP4) in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qba
TitleCrystal Structure of Retinol-Binding Protein 4 (RBP4) in complex with non-retinoid ligand A1120 and engineered binding scaffold
Components
  • DNA-binding protein 7a
  • Retinol-binding protein 4
KeywordsTRANSPORT PROTEIN / Lipocalin / RBP4 / Retinol binding protein
Function / homology
Function and homology information


Retinoid metabolism disease events / Defective visual phototransduction due to STRA6 loss of function / 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 ...Retinoid metabolism disease events / Defective visual phototransduction due to STRA6 loss of function / 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 / retinal binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / cardiac muscle tissue development / retinol metabolic process / retinol binding / positive regulation of immunoglobulin production / The canonical retinoid cycle in rods (twilight vision) / uterus development / vagina development / response to retinoic acid / Retinoid metabolism and transport / RNA endonuclease activity / visual perception / gluconeogenesis / lung development / positive regulation of insulin secretion / glucose homeostasis / heart development / DNA binding / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Retinol binding protein/Purpurin / DNA-binding 7kDa protein / 7kD DNA-binding domain / Lipocalin, ApoD type / Lipocalin family conserved site / Chromo-like domain superfamily / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin ...Retinol binding protein/Purpurin / DNA-binding 7kDa protein / 7kD DNA-binding domain / Lipocalin, ApoD type / Lipocalin family conserved site / Chromo-like domain superfamily / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-2T1 / ACETATE ION / IMIDAZOLE / DI(HYDROXYETHYL)ETHER / Retinol-binding protein 4 / DNA-binding protein 7a
Similarity search - Component
Biological speciesHomo sapiens (human)
Sulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMlynek, G. / Brey, C.U. / Djinovic-Carugo, K. / Puehringer, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: A conformation-specific ON-switch for controlling CAR T cells with an orally available drug.
Authors: Zajc, C.U. / Dobersberger, M. / Schaffner, I. / Mlynek, G. / Puhringer, D. / Salzer, B. / Djinovic-Carugo, K. / Steinberger, P. / De Sousa Linhares, A. / Yang, N.J. / Obinger, C. / Holter, W. ...Authors: Zajc, C.U. / Dobersberger, M. / Schaffner, I. / Mlynek, G. / Puhringer, D. / Salzer, B. / Djinovic-Carugo, K. / Steinberger, P. / De Sousa Linhares, A. / Yang, N.J. / Obinger, C. / Holter, W. / Traxlmayr, M.W. / Lehner, M.
History
DepositionDec 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Retinol-binding protein 4
B: DNA-binding protein 7a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,28213
Polymers28,1832
Non-polymers1,09911
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-78 kcal/mol
Surface area12260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.456, 77.614, 80.509
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Retinol-binding protein 4 / Plasma retinol-binding protein / RBP


Mass: 21251.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP4, PRO2222 / Production host: Komagataella pastoris (fungus) / References: UniProt: P02753
#2: Protein DNA-binding protein 7a / 7 kDa DNA-binding protein a / Endoribonuclease P2 / p7ss


Mass: 6930.735 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: sso7a1, sso7d-2, SSO9180, sso7a2, sso7d-3, SSO9535 / Production host: Escherichia coli (E. coli)
References: UniProt: P61991, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters

-
Non-polymers , 6 types, 220 molecules

#3: Chemical ChemComp-2T1 / 2-[({4-[2-(trifluoromethyl)phenyl]piperidin-1-yl}carbonyl)amino]benzoic acid


Mass: 392.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19F3N2O3
#4: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.63 % / Description: 15x15x300 um
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Zn acetate 0.1 M imidazole pH 8 20% PEG 3K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.968 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 29, 2018
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.8→40.25 Å / Num. obs: 26332 / % possible obs: 99.27 % / Redundancy: 6.7 % / Biso Wilson estimate: 28.59 Å2 / Net I/σ(I): 9.65
Reflection shellResolution: 1.8→1.913 Å / Redundancy: 7 % / Mean I/σ(I) obs: 0.88 / Num. unique obs: 4317 / Rrim(I) all: 1.98 / % possible all: 99.68

-
Processing

Software
NameVersionClassification
PHENIXdev_3353refinement
XDSdata reduction
PHASERphasing
EDNAdata collection
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O9S, 1XYI

4o9s

1xyi


Resolution: 1.8→40.25 Å / SU ML: 0.2346 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.1867
RfactorNum. reflection% reflection
Rfree0.2207 1679 6.38 %
Rwork0.1881 --
obs0.1901 26327 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.65 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1906 0 67 209 2182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672012
X-RAY DIFFRACTIONf_angle_d0.90972704
X-RAY DIFFRACTIONf_chiral_restr0.0508272
X-RAY DIFFRACTIONf_plane_restr0.0044355
X-RAY DIFFRACTIONf_dihedral_angle_d7.96731170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.34731320.33742035X-RAY DIFFRACTION99.36
1.85-1.910.32191400.31172009X-RAY DIFFRACTION100
1.91-1.980.27461490.26712024X-RAY DIFFRACTION99.77
1.98-2.060.25951300.24462030X-RAY DIFFRACTION99.68
2.06-2.150.25621370.23052050X-RAY DIFFRACTION99.73
2.15-2.270.2431370.21792042X-RAY DIFFRACTION99.95
2.27-2.410.24021430.2012050X-RAY DIFFRACTION99.86
2.41-2.60.21181360.19032040X-RAY DIFFRACTION98.24
2.6-2.860.22841300.17561972X-RAY DIFFRACTION95.2
2.86-3.270.18721490.15942067X-RAY DIFFRACTION99.91
3.27-4.120.19481450.15592106X-RAY DIFFRACTION100
4.12-40.260.20751510.17072223X-RAY DIFFRACTION99.75
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)
10.6739307351140.229487203059-1.316305157932.729074255931.021961356353.57712105622-0.2360687941590.7855194903820.477269958127-0.4296739352960.08984950460980.792411559724-0.558228067881-0.575683979558-0.4834618133070.322095329399-0.0559453215319-0.09149214195770.5847484481820.1584544633460.2633524438486.5479935781537.665342873416.8030906076
23.75860579152-2.63779205814-1.327660874274.461878024841.189583644812.65313961383-0.08685900658380.03637952809050.175144147291-0.1550491869910.2170308235440.270800900251-0.127666278736-0.394314972484-0.08266110745330.282827999579-0.0270713697684-0.02439832526810.273841610160.03797792682240.3069824575868.2952283216930.540043209332.0466053735
32.45237795391.091298486381.405579620662.73476009329-1.363739043562.56545178965-0.112076656230.0460179899736-0.358759474505-0.2259295901490.0360630764068-0.2399530545740.1911773931080.4440479027740.1387504972230.2492721321330.0327992283394-0.0174281686780.2794171626850.008903475448540.28706659219919.747760463927.743218527931.7780770402
42.97076389474-2.367970497040.9281498291171.90474461969-0.7019023053110.695970470574-0.001275412854750.134860937740.6348558158120.265022876404-0.06725671161690.351187054925-0.695085225733-0.0488641162962-0.1239376201760.4452263082130.05181715081220.001233568895510.2301748717140.03454130555830.4868492058918.2632901284547.127122423133.9742731362
52.44936553299-1.870720854310.8823557939684.00138310719-1.834186757691.64831373213-0.129581683523-0.231286048975-0.0990308554370.1595867187860.2356984473970.43445827695-0.118188271714-0.219453522802-0.1481647181220.210713587516-0.00497922081999-0.02773854410970.184792164270.009608552343480.26182747311519.835455255430.462849564538.5694886255
61.12677623876-0.5419955325530.05503501859852.51307746859-1.464148412072.55540702311-0.128661030722-0.1990662618590.2399457840940.2882182025350.273334988830.0110313900498-0.332648788496-0.201085751176-0.1879081292420.25632505199-0.0163836723352-0.01714498395620.128660474168-0.0004084504805390.30717581659918.894570303337.502410252336.4930012838
74.30231451749-1.294898215662.923641262551.01187090718-1.307646903934.61794096279-0.1811233245610.5221641673710.8220221504790.0913045506922-0.0956124228195-0.126769529111-0.4774186812360.2117703199630.3084926855860.342751883541-0.0189330164108-0.04013435145890.2705385004630.1326181571630.45146708053315.42743328144.647503140124.630880043
82.12344078315-0.8050484766051.289321961261.0398410103-1.193413546813.46343003712-0.258440001930.01790795277030.267529201433-0.05801390182040.1152183874720.00494346387579-0.380665348831-0.1950208387250.1038270479750.2679415090120.0112416755966-0.02239244148890.2138424793150.01099455528490.29876967739517.898231107738.711928164729.2438111406
91.317028225560.229532772411-0.194665646571.16619846501-0.5195391022281.48966122511-0.14670710530.2765018216820.140806316477-0.1480090214170.1477683333490.0901303956665-0.0106245340657-0.10139394224-0.02489701713930.254659361325-0.0368952734512-0.04099946499240.2655124346110.05436901686090.25353569285310.891799069232.098807846423.6676431674
102.464504629971.08484371101-1.884526609582.48493159868-1.199237258553.52929181049-0.2159713020951.02374384112-0.754047507431-0.367058813150.5391807220080.4661124499361.03358835535-1.09158664907-0.1780319591640.431863889146-0.177335840074-0.05792305909420.623564358460.07462086917140.3701131586961.7614381766725.576269146319.8926102606
112.42899920212-0.0695837115264-1.226917435052.67896721616-1.914425652423.72431481790.06290080094610.3718814698730.00243768092316-0.5491526265210.263770099161-0.1814627585071.211210976770.0122151698613-0.06738499683240.413416364073-0.08986134441760.01246855925950.277762645427-0.04440059138420.30317425692712.578567143123.100377012722.1057913336
123.826285901692.677531818234.226895517988.800065944270.9346867185095.2756177312-0.412785904066-0.5601987259380.313841356729-0.07673283252740.1101763398830.498342472492-0.1868161738090.2645159501680.2162375577850.320599975228-0.007270459782890.02426241831170.328592710102-0.009047236459210.28262917203911.747005125826.300843899143.7594371386
136.887188365962.839826698250.9822211397853.224578764460.202314548313.214099089860.166051503019-0.0502152165710.004165942580620.355512171576-0.03960085906270.104371071366-0.2017275091440.78802370816-0.235850005750.322336622538-0.01657945452580.009036411474440.333649814842-0.07864758873480.27947401491435.571478589939.334962371152.3094277227
143.64813431981-0.307473317994.27198650370.387654216733-0.2585622697465.19031728468-0.0611152647069-0.5589012946410.1239929514970.471616306248-0.0622831204370.160184764712-0.3669598911430.3146262045550.1244475181670.3900941572-0.0986959615450.02515222238880.490270416905-0.1497319311790.42021795539430.216510159740.650685653653.3093470201
155.442879988075.393144811040.669995107245.445715081471.269489174155.291801174430.265794413604-0.576977672167-0.5311802782510.538065618137-0.56026585852-0.4618338924830.3965259854410.394494588281-0.1699929595510.4301271450930.0592129861537-0.04030716593880.4068476852850.04581357071390.26196328298837.087798446129.684465884455.0819053166
167.31984979293-1.001122166381.028969963424.458265334722.020197490923.49957623695-0.0192187999308-0.177258406878-0.04932756928260.1213908084760.02766588703210.1909829340150.133912890135-0.2120110456070.03953210002870.226082927826-0.00761012541644-0.01548610729780.193070263207-0.008514700572380.23085336545129.536588108329.939506778545.743107836
172.7262191831.71233331926-1.57318084441.983307411060.4070910639973.36160999589-0.2344525304330.011442375032-0.0213375394286-0.2037838529470.455810947288-0.4551462196650.1775971669880.2331482011140.1319073981180.289361721211-0.00280451416118-0.0006591076662880.210454091828-0.08276380739180.37727761419238.093734502737.542498319141.5199151516
186.67275367654-0.366104037963-0.6413129531670.424063791670.7228892304627.77301360163-0.316128807844-0.5443882979950.1107859435120.2786441097520.44978232604-0.3412475832710.1558187387861.30825513289-0.1329070033710.3480809655480.0794321703592-0.01719085648310.492682633453-0.001712781088840.33069366891442.698495758127.749925100145.5690553628
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 21 )
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 30 )
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 41 )
4X-RAY DIFFRACTION4chain 'A' and (resid 42 through 52 )
5X-RAY DIFFRACTION5chain 'A' and (resid 53 through 66 )
6X-RAY DIFFRACTION6chain 'A' and (resid 67 through 79 )
7X-RAY DIFFRACTION7chain 'A' and (resid 80 through 92 )
8X-RAY DIFFRACTION8chain 'A' and (resid 93 through 109 )
9X-RAY DIFFRACTION9chain 'A' and (resid 110 through 145 )
10X-RAY DIFFRACTION10chain 'A' and (resid 146 through 158 )
11X-RAY DIFFRACTION11chain 'A' and (resid 159 through 168 )
12X-RAY DIFFRACTION12chain 'A' and (resid 169 through 176 )
13X-RAY DIFFRACTION13chain 'B' and (resid 1 through 7 )
14X-RAY DIFFRACTION14chain 'B' and (resid 8 through 14 )
15X-RAY DIFFRACTION15chain 'B' and (resid 15 through 20 )
16X-RAY DIFFRACTION16chain 'B' and (resid 21 through 42 )
17X-RAY DIFFRACTION17chain 'B' and (resid 43 through 51 )
18X-RAY DIFFRACTION18chain 'B' and (resid 52 through 61 )

+
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