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- PDB-6qba: Crystal Structure of Retinol-Binding Protein 4 (RBP4) in complex ... -

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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 / 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 / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / retinal binding / retinol metabolic process / retinol binding / positive regulation of immunoglobulin production / Retinoid cycle disease events / 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 / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding 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 / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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 / Imidazole


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


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 / Acetate


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


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

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Experimental details

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Experiment

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

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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

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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

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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 )

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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

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