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- PDB-4zps: Crystal Structure of Protocadherin Gamma A8 EC1-3 -

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Basic information

Entry
Database: PDB / ID: 4zps
TitleCrystal Structure of Protocadherin Gamma A8 EC1-3
ComponentsMCG133388, isoform CRA_m
KeywordsCELL ADHESION
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
alpha-D-mannopyranose / Protocadherin gamma A8
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGoodman, K.M. / Mannepalli, S. / Shapiro, L.
CitationJournal: Cell / Year: 2015
Title: Molecular Logic of Neuronal Self-Recognition through Protocadherin Domain Interactions.
Authors: Rubinstein, R. / Thu, C.A. / Goodman, K.M. / Wolcott, H.N. / Bahna, F. / Mannepalli, S. / Ahlsen, G. / Chevee, M. / Halim, A. / Clausen, H. / Maniatis, T. / Shapiro, L. / Honig, B.
History
DepositionMay 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MCG133388, isoform CRA_m
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,43010
Polymers35,7891
Non-polymers6419
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.060, 78.120, 167.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein MCG133388, isoform CRA_m / Protein Pcdhga8 / Protocadherin gamma A8 / Protocadherin gamma subfamily A / 8


Mass: 35789.027 Da / Num. of mol.: 1 / Fragment: UNP residues 30-342
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcdhga8, mCG_133388 / Production host: Homo sapiens (human) / References: UniProt: Q91XY0
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.93 Å3/Da / Density % sol: 58.04 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.7 / Details: 28% PEG400, 100mM Tris-Cl, pH 8.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→45 Å / Num. obs: 9489 / % possible obs: 98.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 44.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.2
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.2 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→42.651 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2865 474 5 %
Rwork0.2644 --
obs0.2657 9489 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→42.651 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2367 0 29 20 2416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032430
X-RAY DIFFRACTIONf_angle_d0.613307
X-RAY DIFFRACTIONf_dihedral_angle_d11.252912
X-RAY DIFFRACTIONf_chiral_restr0.024394
X-RAY DIFFRACTIONf_plane_restr0.003439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.31950.35631460.31532894X-RAY DIFFRACTION97
3.3195-4.18170.291580.27233033X-RAY DIFFRACTION100
4.1817-42.65540.25951700.23953088X-RAY DIFFRACTION98
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)
12.7265-0.2678-0.53253.21861.18361.5341-0.1958-0.31040.10510.72450.7336-0.05250.52040.4885-0.58290.95050.1401-0.13831.0042-0.0730.4546-11.3141-16.109-21.4789
22.3753-0.6813-0.23332.52470.02764.60050.81430.55-0.0769-1.6738-0.45940.4844-0.1178-0.2691-0.1641.26060.2849-0.24450.4744-0.05980.32983.0811-7.59620.5055
31.0736-0.4031-0.51432.73860.19168.1552-0.2258-0.20960.0389-0.00120.1440.04160.03150.20360.10270.1668-0.0941-0.00310.35240.03120.30559.7787-11.499570.4944
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 1:96))
2X-RAY DIFFRACTION2chain 'A' and ((resseq 97:205))
3X-RAY DIFFRACTION3chain 'A' and ((resseq 206:313))

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