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

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Basic information

Entry
Database: PDB / ID: 4zpq
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 / MOLECULAR REPLACEMENT / Resolution: 3.099 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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.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 / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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
C: MCG133388, isoform CRA_f
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,03330
Polymers105,7233
Non-polymers3,31127
Water30617
1
A: MCG133388, isoform CRA_f
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,20910
Polymers35,2411
Non-polymers9689
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MCG133388, isoform CRA_f
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,41210
Polymers35,2411
Non-polymers1,1719
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: MCG133388, isoform CRA_f
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,41210
Polymers35,2411
Non-polymers1,1719
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)190.806, 104.916, 80.066
Angle α, β, γ (deg.)90.00, 97.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 3 molecules ABC

#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.: 3 / 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 , 3 types, 9 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
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 6
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 , 2 types, 35 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.76 Å3/Da / Density % sol: 67.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 16% (w/v) PEG 6000, 200mM calcium acetate, 100mM imidazole, pH 8.0

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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: 3.099→40 Å / Num. obs: 26871 / % possible obs: 94.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 56.8 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.5 / % possible all: 76.2

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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: 3.099→29.192 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2523 1347 5.01 %
Rwork0.2148 --
obs0.2167 26860 93.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.099→29.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6969 0 184 17 7170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027276
X-RAY DIFFRACTIONf_angle_d0.5859947
X-RAY DIFFRACTIONf_dihedral_angle_d11.1442669
X-RAY DIFFRACTIONf_chiral_restr0.0241211
X-RAY DIFFRACTIONf_plane_restr0.0031313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.099-3.20960.33871070.28741977X-RAY DIFFRACTION73
3.2096-3.33790.36161110.28352246X-RAY DIFFRACTION84
3.3379-3.48960.31521190.26612443X-RAY DIFFRACTION90
3.4896-3.67330.24041370.22942599X-RAY DIFFRACTION96
3.6733-3.90290.26681380.23082657X-RAY DIFFRACTION99
3.9029-4.20350.26221300.19942717X-RAY DIFFRACTION100
4.2035-4.6250.23121400.1842689X-RAY DIFFRACTION100
4.625-5.29080.19871650.18392695X-RAY DIFFRACTION100
5.2908-6.65280.25131470.21252729X-RAY DIFFRACTION100
6.6528-29.19380.23521530.20132761X-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)
15.6629-6.7953-0.56918.3881.78111.90340.09150.7845-0.2715-0.1901-0.2692-0.39230.42590.10590.16890.50740.15610.08940.53930.03380.562837.0192-65.213183.5789
20.0403-0.12260.56542.34770.08645.06940.4197-2.28180.69251.6805-0.0087-0.2437-0.6318-0.6426-0.18511.24550.02-0.17442.1837-0.39790.478723.54-38.5176112.7821
31.72491.6867-0.33781.7594-0.44670.2827-0.49470.4449-1.6839-0.25590.0226-0.1491.0466-0.45830.07670.9919-0.54430.15341.0122-0.31042.523-19.6182-90.111454.2573
48.8512-5.13861.75535.4179-2.01552.3804-0.0571-0.19590.21910.06190.0332-0.13140.0029-0.10290.03330.2526-0.020.01490.35960.0440.1556-0.049-40.582188.2251
53.5730.28012.20071.08061.50038.9401-0.12330.01320.2356-0.26080.1656-0.1249-0.24210.15150.00340.2364-0.11280.02720.33040.0230.361418.6866-41.121568.7179
67.03292.94530.76324.56191.34172.73020.15710.0913-1.4396-0.0929-0.1208-0.25280.19560.1378-0.05940.43950.0112-0.01430.4396-0.12970.603516.2882-64.020255.051
75.9696-3.935-1.13565.1049-0.34741.05090.03210.2362.17740.14670.2238-0.4292-0.20750.1407-0.13380.57350.0993-0.00290.66780.08771.4217-35.1911-5.80785.44
81.13240.05212.65820.13121.00294.76720.2329-0.2793-0.3945-0.06050.1340.10630.1563-0.594-0.38780.5432-0.1541-0.00950.6550.07850.40472.3555-53.022426.6973
94.59082.33690.41513.21290.36611.87010.1779-1.50450.09590.4841-0.574-0.7857-0.81441.84040.03190.9226-0.8426-0.26531.85660.13971.329253.1296-39.448367.4531
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 97 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 97 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 97 )
4X-RAY DIFFRACTION4chain 'A' and (resid 98 through 206 )
5X-RAY DIFFRACTION5chain 'B' and (resid 98 through 206 )
6X-RAY DIFFRACTION6chain 'C' and (resid 98 through 206 )
7X-RAY DIFFRACTION7chain 'A' and (resid 207 through 314 )
8X-RAY DIFFRACTION8chain 'B' and (resid 207 through 312 )
9X-RAY DIFFRACTION9chain 'C' and (resid 207 through 311 )

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