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

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Basic information

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


homophilic cell-cell adhesion / synapse organization / negative regulation of neuron apoptotic process / 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, 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 / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / Protocadherin gamma-C5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.002 Å
AuthorsWolcott, H.N. / Goodman, K.M. / Bahna, F. / 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 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 / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.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 / _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
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,53220
Polymers70,4822
Non-polymers2,05018
Water77543
1
A: MCG133388, isoform CRA_f
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,26610
Polymers35,2411
Non-polymers1,0259
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MCG133388, isoform CRA_f
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,26610
Polymers35,2411
Non-polymers1,0259
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.188, 84.563, 109.144
Angle α, β, γ (deg.)90.00, 106.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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.: 2 / 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
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#4: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.22 Å3/Da / Density % sol: 70.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25.5% (w/v) PEG 4000, 15% (v/v) glycerol, 3mM calcium chloride, 85mM Tris-Cl, pH 8.5

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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: Jul 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 23383 / % possible obs: 99.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 74.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.8
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.8 / % possible all: 93.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZPO

4zpo


Resolution: 3.002→27.938 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2481 1202 5.14 %
Rwork0.2095 --
obs0.2115 23383 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.002→27.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4438 0 112 43 4593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034649
X-RAY DIFFRACTIONf_angle_d0.5946370
X-RAY DIFFRACTIONf_dihedral_angle_d10.0731655
X-RAY DIFFRACTIONf_chiral_restr0.025768
X-RAY DIFFRACTIONf_plane_restr0.003860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0024-3.12240.36251060.28862325X-RAY DIFFRACTION94
3.1224-3.26430.29171420.23642442X-RAY DIFFRACTION100
3.2643-3.43610.2951280.24472460X-RAY DIFFRACTION100
3.4361-3.6510.25151240.21812491X-RAY DIFFRACTION100
3.651-3.93220.24051380.20472474X-RAY DIFFRACTION100
3.9322-4.32660.22481430.19362488X-RAY DIFFRACTION100
4.3266-4.94960.23821440.18532476X-RAY DIFFRACTION100
4.9496-6.22460.26691380.21422487X-RAY DIFFRACTION100
6.2246-27.9390.22361390.20222538X-RAY DIFFRACTION99
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)
11.378-0.0763-0.24886.52281.52674.68050.30550.2954-1.4334-0.4277-0.56951.30310.82090.08230.21410.77880.1781-0.18820.7358-0.11971.796964.7813-22.5322114.9011
20.98270.2883-1.77320.3378-0.90134.52240.40330.34810.17630.0134-0.4575-0.2037-0.62781.91760.09921.90130.06480.31182.45070.16950.775557.476441.591955.6582
36.3589-5.8569-1.05989.35711.20391.78460.0671-0.1245-0.02130.5330.1648-0.6899-0.01150.0797-0.18720.62790.0912-0.14990.4871-0.07940.634848.303923.1711118.0534
43.4626-0.9813-3.69092.85480.71789.6589-0.1230.1235-0.108-0.330.08290.34320.4721-0.01520.06820.5110.0613-0.07070.4359-0.02860.506133.386532.188196.856
56.4739-1.669-0.93958.5793-0.71655.9816-0.28390.0150.25520.30220.1350.5962-0.3274-0.13170.13070.49470.04680.06330.4238-0.02720.413322.307859.7959113.6449
61.45321.05-1.45420.8132-0.72064.0264-0.4241-1.8623-0.97091.30950.5710.72660.75190.15830.12311.83290.47110.53631.50780.46270.893322.117427.527138.986
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and resid 207 through 311
2X-RAY DIFFRACTION2chain 'B' and resid 207 through 311
3X-RAY DIFFRACTION3chain 'A' and resid 98 through 206
4X-RAY DIFFRACTION4chain 'B' and resid 98 through 206
5X-RAY DIFFRACTION5chain 'A' and resid 1 through 97
6X-RAY DIFFRACTION6chain 'B' and resid 1 through 97

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