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- PDB-4zpn: Crystal Structure of Protocadherin Gamma C5 EC1-3 with extended N... -

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Basic information

Entry
Database: PDB / ID: 4zpn
TitleCrystal Structure of Protocadherin Gamma C5 EC1-3 with extended N-terminus
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: 3.3 Å
AuthorsGoodman, K.M. / Wolcott, H.N. / Bahna, F. / 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 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,71423
Polymers71,4552
Non-polymers2,26021
Water0
1
A: MCG133388, isoform CRA_f
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,93911
Polymers35,7271
Non-polymers1,21110
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MCG133388, isoform CRA_f
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,77612
Polymers35,7271
Non-polymers1,04811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.027, 108.874, 86.612
Angle α, β, γ (deg.)90.00, 101.61, 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: 35727.406 Da / Num. of mol.: 2 / Fragment: UNP residues 25-345
Source method: isolated from a genetically manipulated source
Details: Construct includes five N-terminal residues from the predicted signal sequence (GWVSG)
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcdhgc5, mCG_133388 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q91XW9
#2: 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.: 1
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
#3: 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: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Ca
#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.: 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

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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: 3.3 Å3/Da / Density % sol: 62.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 8% (w/v) PEG3350, 200mM potassium nitrate, 3% (v/v) glycerol

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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 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.3→108.87 Å / Num. obs: 13905 / % possible obs: 99 % / Redundancy: 3.8 % / Biso Wilson estimate: 73 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.6
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PZO

4pzo


Resolution: 3.3→66.921 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2522 694 5 %Random selection
Rwork0.2111 ---
obs0.2132 13880 98.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→66.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4668 0 121 0 4789
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034872
X-RAY DIFFRACTIONf_angle_d0.7186675
X-RAY DIFFRACTIONf_dihedral_angle_d11.4361742
X-RAY DIFFRACTIONf_chiral_restr0.026818
X-RAY DIFFRACTIONf_plane_restr0.003879
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.55480.30341380.2982629X-RAY DIFFRACTION99
3.5548-3.91250.32961400.23652636X-RAY DIFFRACTION99
3.9125-4.47850.23511370.19852621X-RAY DIFFRACTION99
4.4785-5.6420.25731400.18842652X-RAY DIFFRACTION99
5.642-66.93460.20721390.19432648X-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)
13.73060.3453-0.28997.90270.7665.31750.6683-0.2655-0.24151.105-0.2695-0.12420.4417-0.2755-0.28310.8112-0.0448-0.01290.33450.06830.543350.9157-33.730236.6248
25.67971.1851-2.48652.9416-0.50996.3689-0.33660.2175-0.1363-0.01320.04510.00170.43540.76950.24880.67470.14130.04210.5364-0.01060.335755.2953-4.33134.2548
32.9003-2.80210.02038.20930.22441.56510.04770.28220.444-0.0693-0.2483-0.66010.05870.1640.20150.74580.03640.2150.36660.05680.49449.907210.238132.183
44.9810.3281-2.50020.6822-1.11333.81490.41550.50920.266-0.3486-0.0416-0.1234-0.7738-0.9254-0.37650.5820.10330.17720.33770.00290.511930.8292-8.901741.0859
54.31832.9156-1.11813.7714-2.39293.88580.01620.29990.57380.027-0.22810.3555-0.368-0.56860.38270.86860.11840.13630.4638-0.06930.718137.815657.797124.9317
62.92961.2519-1.39092.3535-0.47135.3603-0.2763-1.183-0.0350.14290.1219-0.3114-0.00220.17850.15440.62370.35930.01541.0604-0.07420.494310.4867-5.75287.4379
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 1:102))
2X-RAY DIFFRACTION2chain 'B' and ((resseq 2:102))
3X-RAY DIFFRACTION3chain 'A' and ((resseq 103:211))
4X-RAY DIFFRACTION4chain 'B' and ((resseq 103:211))
5X-RAY DIFFRACTION5chain 'A' and ((resseq 212:320))
6X-RAY DIFFRACTION6chain 'B' and ((resseq 212:321))

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