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- PDB-4zpo: Crystal Structure of Protocadherin Gamma C5 EC1-3 -

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Basic information

Entry
Database: PDB / ID: 4zpo
TitleCrystal Structure of Protocadherin Gamma C5 EC1-3
ComponentsMCG133388, isoform CRA_f
KeywordsCELL ADHESION
Function / homology
Function and homology information


homophilic cell adhesion via plasma membrane adhesion molecules / synapse organization / negative regulation of neuron apoptotic process / 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 / Pcdhgc5 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.9 Å
AuthorsWolcott, H.N. / Goodman, K.M. / Bahna, F. / Mannepalli, S. / Rubinstein, R. / Honig, B. / 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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 / _pdbx_struct_special_symmetry.label_asym_id / _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_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 / _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_f
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,32711
Polymers35,2411
Non-polymers1,08610
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.637, 108.637, 96.614
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-514-

HOH

21A-515-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein MCG133388, isoform CRA_f / Pcdhgc5 protein / Protein Pcdhgc5 / Protocadherin gamma C-V / Protocadherin gamma C5 / ...Pcdhgc5 protein / Protein Pcdhgc5 / Protocadherin gamma C-V / Protocadherin gamma C5 / Protocadherin gamma subfamily C / 5


Mass: 35240.887 Da / Num. of mol.: 1 / Fragment: UNP residues 30-345
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcdhgc5, mCG_133388 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q91XW9

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Sugars , 2 types, 3 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / Mannose


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

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Non-polymers , 3 types, 22 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 4.04 Å3/Da / Density % sol: 69.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 40% (v/v) MPD, 5% (w/v) PEG 8000, 100mM sodium cacodylate, pH 6

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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: Aug 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→30.064 Å / Num. obs: 13086 / % possible obs: 99.9 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.8
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 5.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2.9→30.064 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 31.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2472 678 5.18 %
Rwork0.2202 --
obs0.2216 13086 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→30.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2352 0 60 15 2427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022451
X-RAY DIFFRACTIONf_angle_d0.5143345
X-RAY DIFFRACTIONf_dihedral_angle_d11.639917
X-RAY DIFFRACTIONf_chiral_restr0.022403
X-RAY DIFFRACTIONf_plane_restr0.002441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.12380.27681430.26142259X-RAY DIFFRACTION92
3.1238-3.43770.35831190.27092469X-RAY DIFFRACTION100
3.4377-3.93420.30571240.25082498X-RAY DIFFRACTION100
3.9342-4.95310.23471620.19522507X-RAY DIFFRACTION100
4.9531-30.06570.18571300.19862675X-RAY DIFFRACTION100
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)
16.9033-1.3144-0.26731.4518-0.57861.9104-0.0458-0.5402-1.15110.2969-0.0821-0.53090.14590.35430.14130.4623-0.0588-0.12130.54630.19981.350933.85274.741555.7574
28.35481.13050.20422.66510.73660.80850.1851-0.6424-0.31260.0753-0.04820.10030.0785-0.1441-0.14990.3811-0.0050.02610.5019-0.0020.9924-10.60648.200753.0265
34.39120.79144.39993.31392.46836.1035-0.1307-0.1906-0.5081-0.0671-0.02250.3975-0.1155-0.34490.10550.4875-0.05510.06670.4733-0.02471.3415-58.04078.541139.0011
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and resid 1 through 97
2X-RAY DIFFRACTION2chain 'A' and resid 98 through 206
3X-RAY DIFFRACTION3chain 'A' and resid 207 through 311

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