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- PDB-5szq: Protocadherin Gamma A4 extracellular cadherin domains 3-6 -

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Basic information

Entry
Database: PDB / ID: 5szq
TitleProtocadherin Gamma A4 extracellular cadherin domains 3-6
ComponentsProtocadherin gamma-A4
KeywordsCELL ADHESION
Function / homology
Function and homology information


plasma membrane => GO:0005886 / homophilic cell adhesion via plasma membrane adhesion molecules / spermatogenesis / cell adhesion / calcium ion binding / 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 / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain ...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 / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily
Similarity search - Domain/homology
alpha-D-mannopyranose / Protocadherin gamma-A4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.608 Å
AuthorsGoodman, K.M. / Mannepalli, S. / Bahna, F. / Honig, B. / Shapiro, L.
CitationJournal: Elife / Year: 2016
Title: gamma-Protocadherin structural diversity and functional implications.
Authors: Goodman, K.M. / Rubinstein, R. / Thu, C.A. / Mannepalli, S. / Bahna, F. / Ahlsen, G. / Rittenhouse, C. / Maniatis, T. / Honig, B. / Shapiro, L.
History
DepositionAug 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
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 / 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_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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 / _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 2.1Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protocadherin gamma-A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,14818
Polymers48,0611
Non-polymers2,08717
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.890, 63.640, 344.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protocadherin gamma-A4 / PCDH-gamma-A4


Mass: 48060.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PcdhgA4 extracellular domains 3-6 with C-terminal octahistidine tag
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcdhga4 / Production host: Homo sapiens (human) / References: UniProt: Q91XY4
#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.: 1
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: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-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
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca

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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: 3.63 Å3/Da / Density % sol: 66.16 %
Crystal growTemperature: 295 K / Method: batch mode / pH: 8.5
Details: 0.1 M ammonium sulfate, 9% (w/v) PEG20000, 18% PEG550MME, 0.1 M Morpheus Buffer System 3 (Tris/Bicine; Molecular Dimensions) pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97919 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.56→172.16 Å / Num. obs: 23763 / % possible obs: 99.3 % / Redundancy: 4.1 % / Biso Wilson estimate: 48.68 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.112 / Net I/σ(I): 6.6
Reflection shellResolution: 2.56→2.67 Å / Redundancy: 3.3 % / Rmerge(I) obs: 3.118 / CC1/2: 0.434 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EC3-4 of 5SZM, EC5 of 5SZN and EC6 of 5SZR

5szm

5szn

5szr


Resolution: 2.608→19.957 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 43.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.282 554 4.75 %
Rwork0.2506 --
obs0.2522 11652 51.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.608→19.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3189 0 117 0 3306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043365
X-RAY DIFFRACTIONf_angle_d0.6584618
X-RAY DIFFRACTIONf_dihedral_angle_d15.0932040
X-RAY DIFFRACTIONf_chiral_restr0.048578
X-RAY DIFFRACTIONf_plane_restr0.005591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6084-2.87020.4083200.3529407X-RAY DIFFRACTION8
2.8702-3.28390.4409780.33811778X-RAY DIFFRACTION34
3.2839-4.13140.33241740.29083463X-RAY DIFFRACTION65
4.1314-19.95750.24692820.22265450X-RAY DIFFRACTION97
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)
10.8485-0.1473-0.24620.5841-0.30170.717-0.0631-0.11660.60330.06330.2669-0.2102-0.53280.44540.0490.8950.04060.22210.53280.42220.7031-56.907938.6104-35.9493
20.20870.2157-0.33680.2006-0.37110.5760.14980.6034-0.1636-0.48720.1090.19260.2956-0.0320.00021.1925-0.2970.25162.02050.62410.3256-34.423536.3868-78.2865
31.2822-0.40980.00830.2309-0.32710.93890.076-1.2694-0.26620.13150.0416-0.111-0.05730.8596-0.02750.8632-0.17250.0611.2065-0.15680.5832-22.18750.5989-125.2481
40.4917-0.3551-0.06081.89810.39130.61710.26890.08130.0772-0.1610.06850.0507-0.565-0.03050.17680.30920.11090.0430.0323-0.19230.5945-30.134454.4429-173.205
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 210:312))
2X-RAY DIFFRACTION2chain 'A' and ((resseq 313:417))
3X-RAY DIFFRACTION3chain 'A' and ((resseq 418:527))
4X-RAY DIFFRACTION4chain 'A' and ((resseq 528:637))

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