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- PDB-3ngh: Molecular Analysis of the Interaction of the HDL Receptor SR-BI w... -

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Basic information

Entry
Database: PDB / ID: 3ngh
TitleMolecular Analysis of the Interaction of the HDL Receptor SR-BI with the Adaptor Protein PDZK1
ComponentsPDZ domain-containing protein 1
KeywordsSIGNALING PROTEIN / PDZ domain / Adaptor protein / SR-BI
Function / homology
Function and homology information


positive regulation of protein targeting to membrane / regulation of monoatomic anion transport / protein localization to plasma membrane / brush border membrane / in utero embryonic development / plasma membrane
Similarity search - Function
: / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Na(+)/H(+) exchange regulatory cofactor NHE-RF3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKocher, O. / Birrane, G. / Krieger, M. / Ladias, J.A.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: In vitro and in vivo analysis of the binding of the C terminus of the HDL receptor scavenger receptor class B, type I (SR-BI), to the PDZ1 domain of its adaptor protein PDZK1.
Authors: Kocher, O. / Birrane, G. / Tsukamoto, K. / Fenske, S. / Yesilaltay, A. / Pal, R. / Daniels, K. / Ladias, J.A. / Krieger, M.
History
DepositionJun 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PDZ domain-containing protein 1
B: PDZ domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)23,6772
Polymers23,6772
Non-polymers00
Water3,369187
1
A: PDZ domain-containing protein 1

B: PDZ domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)23,6772
Polymers23,6772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+3/2,-y,z+1/21
Buried area1310 Å2
ΔGint-4 kcal/mol
Surface area12230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.604, 55.114, 111.055
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PDZ domain-containing protein 1 / NHERF-3 / Na(+)/H(+) exchange regulatory cofactor NHE-RF3 / CFTR-associated protein of 70 kDa / ...NHERF-3 / Na(+)/H(+) exchange regulatory cofactor NHE-RF3 / CFTR-associated protein of 70 kDa / Na/Pi cotransporter C-terminal-associated protein 1 / NaPi-Cap1 / Sodium-hydrogen exchanger regulatory factor 3 / Na(+)/H(+) exchanger regulatory factor 3


Mass: 11838.280 Da / Num. of mol.: 2 / Fragment: residues 7-106 / Mutation: C5S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cap70, Nherf3, Pdzk1 / Plasmid: pMal-c2x / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q9JIL4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMOUSE SR-BI PROTEIN AS IN UNP ENTRY Q61009, RESIDUES 505-509

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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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100mM Tris/HCl, 40% PEG 200, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 1, 2009 / Details: mirrors
RadiationMonochromator: Si(111) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.65→30.7 Å / Num. all: 26518 / Num. obs: 26518 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.488 / Rsym value: 0.545 / Net I/σ(I): 41.1
Reflection shellResolution: 1.65→1.86 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.055 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1235 / Rsym value: 0.056 / % possible all: 91.7

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EDZ

2edz


Resolution: 1.8→29.91 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.595 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23763 1003 4.8 %RANDOM
Rwork0.19973 ---
all0.20158 19752 --
obs0.20158 19752 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.334 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.11 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1666 0 0 187 1853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221722
X-RAY DIFFRACTIONr_bond_other_d0.0010.021217
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.992315
X-RAY DIFFRACTIONr_angle_other_deg0.96732987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2095220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.40525.50689
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.27415345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2971513
X-RAY DIFFRACTIONr_chiral_restr0.1230.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021935
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02318
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.11.51062
X-RAY DIFFRACTIONr_mcbond_other0.3351.5444
X-RAY DIFFRACTIONr_mcangle_it1.88721705
X-RAY DIFFRACTIONr_scbond_it2.93660
X-RAY DIFFRACTIONr_scangle_it4.6774.5606
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 63 -
Rwork0.228 1396 -
all-1459 -
obs--97.01 %
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)
10.5701-0.08770.83741.1013-0.36811.5369-0.02390.15680.08930.0808-0.0457-0.0716-0.04630.10460.06960.15210.00030.00450.19190.01010.220132.398-3.22190.962
21.1115-0.43341.18351.2121-0.13071.3843-0.06520.02920.07930.03960.04460.09330.03420.00240.02050.1558-0.00390.0130.19020.01150.201626.377-3.9389.756
3-0.4222-1.347-1.18091.0958-2.70935.8104-0.18240.0113-0.14050.04940.35930.2417-0.5712-0.0321-0.17690.1646-0.033-0.0120.1994-0.04410.262220.5068.34582.664
41.10691.95381.09052.48731.31130.6313-0.10830.060.2139-0.16450.01820.2481-0.09530.18640.09010.2303-0.014-0.07450.2089-0.01520.187630.7477.61462.28
52.22632.86433.59690.36153.03693.2109-0.4213-0.32220.7078-0.3695-0.38850.61220.1411-0.12530.80990.3850.0763-0.13140.0348-0.12630.33622.7253.31663.472
6-0.1002-0.1122-0.25160.49310.66740.53510.0188-0.00090.02420.0855-0.0780.13390.13810.06320.05920.2279-0.0189-0.04210.1784-0.01010.233322.02-0.99558.029
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 40
2X-RAY DIFFRACTION2A41 - 92
3X-RAY DIFFRACTION3A93 - 111
4X-RAY DIFFRACTION4B6 - 25
5X-RAY DIFFRACTION5B26 - 67
6X-RAY DIFFRACTION6B68 - 111

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