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- PDB-5t9t: Protocadherin Gamma B2 extracellular cadherin domains 1-5 -

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Basic information

Entry
Database: PDB / ID: 5t9t
TitleProtocadherin Gamma B2 extracellular cadherin domains 1-5
ComponentsProtocadherin gamma B2-alpha C
KeywordsCELL ADHESION
Function / homology
Function and homology information


homophilic cell adhesion via plasma membrane adhesion molecules / membrane => GO:0016020 / calcium ion binding / 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 / Protocadherin gamma B2-alpha C
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsGoodman, K.M. / Mannepalli, S. / Bahna, F. / Honig, B. / Shapiro, L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 United States
National Institutes of Health/Office of the DirectorOD012351 United States
National Institutes of Health/Office of the DirectorOD021764 United States
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
DepositionSep 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_struct_assembly_auth_evidence / 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_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 2.1Mar 23, 2022Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_audit_support / 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
Revision 2.2Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protocadherin gamma B2-alpha C
B: Protocadherin gamma B2-alpha C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,26143
Polymers118,8412
Non-polymers4,42041
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8830 Å2
ΔGint-99 kcal/mol
Surface area55900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.722, 118.067, 98.190
Angle α, β, γ (deg.)90.00, 103.91, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is dimeric. This was determined by sedimentation equilibrium analytical ultracentrifugation.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Protocadherin gamma B2-alpha C


Mass: 59420.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q8K486

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Sugars , 3 types, 15 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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.: 11
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: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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

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Non-polymers , 2 types, 30 molecules

#3: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.82 Å3/Da / Density % sol: 67.82 %
Crystal growTemperature: 295 K / Method: batch mode / pH: 7.5
Details: 8.3% (w/v) PEG8000, 16.7% (v/v) ethylene glycol, 30 mM magnesium chloride, 30 mM calcium chloride, 0.1 M Morpheus Buffer System 2 (Hepes/MOPS buffer; Molecular Dimensions)

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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: Aug 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.5→40 Å / Num. obs: 22663 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 69.73 Å2 / CC1/2: 0.957 / Rmerge(I) obs: 0.369 / Net I/σ(I): 4.8
Reflection shellResolution: 3.5→3.78 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.176 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.561 / % possible all: 100

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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: 5SZR

5szr


Resolution: 3.5→39.751 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.75
RfactorNum. reflection% reflection
Rfree0.2565 1088 4.81 %
Rwork0.2131 --
obs0.2151 22631 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.5→39.751 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7981 0 238 4 8223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038364
X-RAY DIFFRACTIONf_angle_d0.61311461
X-RAY DIFFRACTIONf_dihedral_angle_d13.8045088
X-RAY DIFFRACTIONf_chiral_restr0.0441391
X-RAY DIFFRACTIONf_plane_restr0.0041512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.65920.36651330.30512666X-RAY DIFFRACTION100
3.6592-3.8520.34731310.29222689X-RAY DIFFRACTION100
3.852-4.09310.28051470.23522679X-RAY DIFFRACTION100
4.0931-4.40880.24681360.21482659X-RAY DIFFRACTION100
4.4088-4.85180.24011390.19492678X-RAY DIFFRACTION100
4.8518-5.55220.25321360.17922719X-RAY DIFFRACTION100
5.5522-6.9890.2711430.21242694X-RAY DIFFRACTION100
6.989-39.7540.1721230.16952759X-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)
10.0556-0.0350.00860.0339-0.00290.0954-0.118-0.12-0.2665-0.0687-0.2413-0.4823-0.1518-0.0524-0.00680.5260.1140.11430.38030.08380.6412-7.9854146.489-78.4155
20.0390.03380.06930.0837-0.01860.09010.27690.237-0.1098-0.0976-0.37220.39090.0210.1186-0.00130.64170.0655-0.0890.3587-0.02570.3834-13.331517.0889-42.6358
30.81740.38220.24510.5076-0.21141.35850.2501-0.10120.1775-0.2022-0.0183-0.37740.1894-0.11220.54220.2075-0.00580.20660.4220.18650.7196-1.9162104.0355-68.7844
40.1305-0.034-0.15860.06780.02530.19610.15970.08940.0301-0.053-0.11-0.06510.3268-0.1425-00.7545-0.0238-0.19660.47630.0390.6695-14.614156.6678-60.9917
50.02230.0447-0.00520.0546-0.01230.0091-0.2208-0.04190.10550.1541-0.0801-0.0537-0.35490.0739-0.01190.4816-0.0925-0.13360.41020.11450.5215-5.529662.0946-41.1242
60.0187-0.0415-0.040.07910.0430.03940.39110.0099-0.10540.2026-0.2605-0.06820.0462-0.0422-00.62760.0178-0.02170.47080.01640.6893-23.262106.9651-62.3503
70.0746-0.05910.06030.0434-0.0540.0661-0.0262-0.22080.05210.0702-0.2962-0.16160.06480.2023-0.63260.1583-0.12830.19860.55980.14890.191-1.744517.5165-19.4249
80.16640.0321-0.16680.0387-0.00970.1652-0.17140.0274-0.055-0.2487-0.10320.116-0.0884-0.0565-00.60270.017-0.06690.45620.00450.443-32.5106154.3026-74.7614
90.083-0.0239-0.08370.88470.61080.4955-0.1208-0.5193-0.0216-0.27330.26080.09110.0032-0.10930.43740.34330.0422-0.05750.62940.18450.3508-14.1347-24.92996.0989
100.0608-0.01710.10740.0259-0.02040.25910.2450.03790.07180.096-0.3821-0.63720.0809-0.1343-0.00020.48620.0624-0.05340.41660.01840.4587-37.0127205.8695-76.6438
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:96 )A2 - 96
2X-RAY DIFFRACTION2( CHAIN B AND RESID 2:96 )B2 - 96
3X-RAY DIFFRACTION3( CHAIN A AND RESID 97:204 )A97 - 204
4X-RAY DIFFRACTION4( CHAIN B AND RESID 97:204 )B97 - 204
5X-RAY DIFFRACTION5( CHAIN A AND RESID 205:310 )A205 - 310
6X-RAY DIFFRACTION6( CHAIN B AND RESID 205:310 )B205 - 310
7X-RAY DIFFRACTION7( CHAIN A AND RESID 311:415 )A311 - 415
8X-RAY DIFFRACTION8( CHAIN B AND RESID 311:415 )B311 - 415
9X-RAY DIFFRACTION9( CHAIN A AND RESID 416:525 )A416 - 525
10X-RAY DIFFRACTION10( CHAIN B AND RESID 416:527 )B416 - 527

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