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- PDB-4zi9: Structure of mouse clustered PcdhgA1 EC1-3 -

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Basic information

Entry
Database: PDB / ID: 4zi9
TitleStructure of mouse clustered PcdhgA1 EC1-3
ComponentsMCG133388, isoform CRA_t
KeywordsCELL ADHESION / protocadherin / complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


homophilic cell adhesion via plasma membrane adhesion molecules / cell adhesion / calcium ion binding / membrane / plasma membrane
Similarity search - Function
Cadherin, C-terminal catenin-binding domain / Cadherin C-terminal cytoplasmic tail, catenin-binding region / Cadherin, cytoplasmic C-terminal domain / Cadherin cytoplasmic C-terminal / Cadherin, N-terminal / Cadherin-like / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. ...Cadherin, C-terminal catenin-binding domain / Cadherin C-terminal cytoplasmic tail, catenin-binding region / Cadherin, cytoplasmic C-terminal domain / Cadherin cytoplasmic C-terminal / Cadherin, N-terminal / Cadherin-like / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protocadherin gamma A1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsNicoludis, J.M. / Lau, S.-Y. / Scharfe, C.P.I. / Marks, D.S. / Weihofen, W.A. / Gaudet, R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103403 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10 RR029205 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Structure / Year: 2015
Title: Structure and Sequence Analyses of Clustered Protocadherins Reveal Antiparallel Interactions that Mediate Homophilic Specificity.
Authors: Nicoludis, J.M. / Lau, S.Y. / Scharfe, C.P. / Marks, D.S. / Weihofen, W.A. / Gaudet, R.
History
DepositionApr 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Nov 18, 2015Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MCG133388, isoform CRA_t
B: MCG133388, isoform CRA_t
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,31114
Polymers70,8302
Non-polymers48112
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-73 kcal/mol
Surface area31800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.751, 63.687, 107.486
Angle α, β, γ (deg.)90.00, 99.69, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid BB0

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Components

#1: Protein MCG133388, isoform CRA_t / Protein Pcdhga1 / Protocadherin gamma A1


Mass: 35414.801 Da / Num. of mol.: 2 / Fragment: UNP residues 29-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcdhga1, mCG_133388 / Plasmid: pSpeedET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-Gold / References: UniProt: Q91XZ0
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 3.23 Å3/Da / Density % sol: 61.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM Tris pH 8.5, 7.5% PEG8000, 200 mM NDSB-221 / PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.7→33.51 Å / Num. obs: 81585 / % possible obs: 80 % / Redundancy: 5.42 % / Biso Wilson estimate: 22.65 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 5.42
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 0.33 / % possible all: 36

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2wcp

2wcp


Resolution: 1.7→33.51 Å / Cross valid method: FREE R-VALUE / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2663 2120 -random selection
Rwork0.2298 ---
obs0.2307 81585 80 %-
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.6 Å2
Refinement stepCycle: LAST / Resolution: 1.7→33.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4812 0 12 477 5301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085033
X-RAY DIFFRACTIONf_angle_d1.16842
X-RAY DIFFRACTIONf_chiral_restr0.046779
X-RAY DIFFRACTIONf_plane_restr0.005914
X-RAY DIFFRACTIONf_dihedral_angle_d12.9131930
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2926X-RAY DIFFRACTION5.671TORSIONAL
12B2926X-RAY DIFFRACTION5.671TORSIONAL
LS refinement shellResolution: 1.7→1.7608 Å
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)
10.47960.1990.50181.29250.83910.8571-0.001-0.2716-0.01770.23180.1035-0.21160.05650.8122-0.08480.3556-0.1313-0.00790.93270.00550.249121.854432.546996.591
20.7906-0.0071-0.43740.27570.52332.24490.0971-0.15540.09810.07640.02370.0195-0.0879-0.0258-0.04340.1408-0.11730.01920.24580.08450.019315.350328.701152.0795
30.7191-0.03891.03110.6621-0.24371.52880.02440.25010.1636-0.3852-0.04020.2663-0.2544-0.68430.04570.45410.0565-0.04310.95580.15590.35391.94838.63994.2796
41.606-0.1919-0.29551.1636-0.53841.03060.12460.0495-0.0113-0.09640.02270.1858-0.0401-0.6457-0.12760.2138-0.0721-0.00850.67990.00070.205714.462732.5529-43.1695
50.88680.0151-0.00720.06570.24957.3395-0.08630.0744-0.1945-0.07350.12790.01450.3187-0.0307-0.02380.2618-0.09110.0120.56010.04440.203520.865628.75951.4711
60.22140.10350.06610.3110.40260.7583-0.02450.08260.0012-0.01630.0497-0.00130.08690.0850.15350.0012-0.049-0.00050.1060.0855-0.137334.28838.363449.1633
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 99 )
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 206 )
3X-RAY DIFFRACTION3chain 'A' and (resid 207 through 309 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 99 )
5X-RAY DIFFRACTION5chain 'B' and (resid 100 through 206 )
6X-RAY DIFFRACTION6chain 'B' and (resid 207 through 309 )

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