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- PDB-7zvr: Crystal structure of the carotenoid-binding protein domain from s... -

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Basic information

Entry
Database: PDB / ID: 7zvr
TitleCrystal structure of the carotenoid-binding protein domain from silkworm Bombyx mori (BmCBP) complexed with zeaxanthin
ComponentsCarotenoid-binding protein
KeywordsTRANSPORT PROTEIN / carotenoid-binding protein / carotenoid transport / CBP / STARD / START domain / Bombyx mori
Function / homology
Function and homology information


vesicle tethering to endoplasmic reticulum / endoplasmic reticulum-endosome membrane contact site / cholesterol transport / cholesterol binding / late endosome membrane / lysosomal membrane / endoplasmic reticulum membrane
Similarity search - Function
in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / START-like domain superfamily
Similarity search - Domain/homology
Chem-ZEX / Carotenoid-binding protein
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSluchanko, N.N. / Boyko, K.M. / Varfolomeeva, L.A. / Slonimskiy, Y.B. / Egorkin, N.A. / Maksimov, E.G. / Popov, V.O.
Funding support Russian Federation, Germany, 3items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federation075-15-2021-1354 Russian Federation
Russian Foundation for Basic Research20-54-12018 Russian Federation
German Research Foundation (DFG)FR1276/6-1 Germany
CitationJournal: Structure / Year: 2022
Title: Structural basis for the carotenoid binding and transport function of a START domain.
Authors: Sluchanko, N.N. / Slonimskiy, Y.B. / Egorkin, N.A. / Varfolomeeva, L.A. / Kleymenov, S.Y. / Minyaev, M.E. / Faletrov, Y.V. / Moysenovich, A.M. / Parshina, E.Y. / Friedrich, T. / Maksimov, E. ...Authors: Sluchanko, N.N. / Slonimskiy, Y.B. / Egorkin, N.A. / Varfolomeeva, L.A. / Kleymenov, S.Y. / Minyaev, M.E. / Faletrov, Y.V. / Moysenovich, A.M. / Parshina, E.Y. / Friedrich, T. / Maksimov, E.G. / Boyko, K.M. / Popov, V.O.
History
DepositionMay 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 14, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carotenoid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1002
Polymers28,5311
Non-polymers5691
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.688, 66.528, 120.516
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-509-

HOH

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Components

#1: Protein Carotenoid-binding protein


Mass: 28530.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: BmCBP / Production host: Escherichia coli (E. coli) / References: UniProt: Q8MYA9
#2: Chemical ChemComp-ZEX / (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol


Mass: 568.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.7 M Sodium citrate tribasic dihydrate, 0.1 M BIS-TRIS propane, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jan 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→60.26 Å / Num. obs: 17115 / % possible obs: 98 % / Redundancy: 10.6 % / Biso Wilson estimate: 35.86 Å2 / CC1/2: 0.834 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.043 / Rrim(I) all: 0.133 / Net I/σ(I): 15 / Num. measured all: 180636 / Scaling rejects: 570
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.0510.31.1691246212070.6570.3711.229295.5
8.93-60.264.90.04810462140.9940.0240.05428.293.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.7data scaling
MOLREPphasing
BUSTERrefinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZTQ

7ztq


Resolution: 2→60.26 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.874 / SU R Cruickshank DPI: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.245 / SU Rfree Blow DPI: 0.204 / SU Rfree Cruickshank DPI: 0.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2839 792 4.72 %RANDOM
Rwork0.2351 ---
obs0.2375 16785 96 %-
Displacement parametersBiso max: 97.09 Å2 / Biso mean: 41.54 Å2 / Biso min: 15.31 Å2
Baniso -1Baniso -2Baniso -3
1-6.4326 Å20 Å20 Å2
2--5.5717 Å20 Å2
3----12.0042 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: final / Resolution: 2→60.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1856 0 20 136 2012
Biso mean--32.88 42.25 -
Num. residues----234
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d688SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes334HARMONIC5
X-RAY DIFFRACTIONt_it1961HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion247SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1771SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1961HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg2667HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion3.55
X-RAY DIFFRACTIONt_other_torsion20.29
LS refinement shellResolution: 2→2.02 Å / Rfactor Rfree error: 0 / Total num. of bins used: 40
RfactorNum. reflection% reflection
Rfree0.2234 18 4.18 %
Rwork0.2618 413 -
all0.2601 431 -
obs--91.3 %
Refinement TLS params.Method: refined / Origin x: 16.3278 Å / Origin y: -12.7813 Å / Origin z: 17.7012 Å
111213212223313233
T-0.0081 Å20.0052 Å2-0.0657 Å2--0.1111 Å20.051 Å2---0.1256 Å2
L1.2548 °2-0.0577 °20.1823 °2-3.889 °20.0694 °2--1.9901 °2
S-0.0873 Å °0.13 Å °0.0581 Å °-0.1052 Å °-0.0557 Å °0.136 Å °-0.0292 Å °-0.0219 Å °0.1429 Å °
Refinement TLS groupSelection details: { A|* }

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