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- PDB-6vg1: xenopus protocadherin 8.1 EC1-6 -

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Basic information

Entry
Database: PDB / ID: 6vg1
Titlexenopus protocadherin 8.1 EC1-6
Componentsprotocadherin protein
KeywordsCELL ADHESION / cadherin / hemophilic
Function / homology
Function and homology information


homophilic cell adhesion via plasma membrane adhesion molecules / calcium ion binding / plasma membrane
Similarity search - Function
Cadherin, N-terminal / Cadherin-like / : / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily
Similarity search - Domain/homology
alpha-D-mannopyranose / MGC84237 protein
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHarrison, O.J. / Brasch, B. / Shapiro, L.S.
Funding support United States, 3items
OrganizationGrant numberCountry
Other privateR01MH114817 United States
Other privateR01GM118584 United States
Other privateMCB-1412472 United States
CitationJournal: Cell Rep / Year: 2020
Title: Family-wide Structural and Biophysical Analysis of Binding Interactions among Non-clustered δ-Protocadherins.
Authors: Oliver J Harrison / Julia Brasch / Phinikoula S Katsamba / Goran Ahlsen / Alex J Noble / Hanbin Dan / Rosemary V Sampogna / Clinton S Potter / Bridget Carragher / Barry Honig / Lawrence Shapiro /
Abstract: Non-clustered δ1- and δ2-protocadherins, close relatives of clustered protocadherins, function in cell adhesion and motility and play essential roles in neural patterning. To understand the ...Non-clustered δ1- and δ2-protocadherins, close relatives of clustered protocadherins, function in cell adhesion and motility and play essential roles in neural patterning. To understand the molecular interactions underlying these functions, we used solution biophysics to characterize binding of δ1- and δ2-protocadherins, determined crystal structures of ectodomain complexes from each family, and assessed ectodomain assembly in reconstituted intermembrane junctions by cryoelectron tomography (cryo-ET). Homophilic trans (cell-cell) interactions were preferred for all δ-protocadherins, with additional weaker heterophilic interactions observed exclusively within each subfamily. As expected, δ1- and δ2-protocadherin trans dimers formed through antiparallel EC1-EC4 interfaces, like clustered protocadherins. However, no ectodomain-mediated cis (same-cell) interactions were detectable in solution; consistent with this, cryo-ET of reconstituted junctions revealed dense assemblies lacking the characteristic order observed for clustered protocadherins. Our results define non-clustered protocadherin binding properties and their structural basis, providing a foundation for interpreting their functional roles in neural patterning.
History
DepositionJan 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
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 / _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_asym_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_asym_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 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: protocadherin protein
B: protocadherin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,29944
Polymers141,6702
Non-polymers3,62942
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, dimer by sedimentation equilibrium AUC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7840 Å2
ΔGint-161 kcal/mol
Surface area71300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.645, 42.393, 167.471
Angle α, β, γ (deg.)90.000, 110.603, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein protocadherin protein


Mass: 70834.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: pcdh8, MGC84237, XELAEV_18013229mg / Production host: Homo sapiens (human) / References: UniProt: Q6GLU2

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Sugars , 2 types, 6 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.: 2
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
#6: 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

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Non-polymers , 5 types, 174 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.48 Å3/Da / Density % sol: 64.62 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.135M nitrate-phosphate-sulfate mix (0.045M sodium phosphate dibasic dihydrate, 0.045M Ammonium sulfate, 0.045 M sodium nitrate; Molecular ...Details: 10% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.135M nitrate-phosphate-sulfate mix (0.045M sodium phosphate dibasic dihydrate, 0.045M Ammonium sulfate, 0.045 M sodium nitrate; Molecular Dimensions), 0.1M MES/imidazole buffer pH 6.5 with no further cryoprotection

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 59475 / % possible obs: 97.5 % / Redundancy: 4.4 % / Biso Wilson estimate: 23.21 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.8
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 5.28 / Num. unique obs: 6132 / CC1/2: 0.37

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VFQ, 6VFV

6vfq

6vfv


Resolution: 2→38.27 Å / SU ML: 0.2979 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.1337
RfactorNum. reflection% reflectionSelection details
Rfree0.2972 1775 3.03 %random
Rwork0.253 ---
obs0.2544 59447 45.03 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 68.64 Å2
Refinement stepCycle: LAST / Resolution: 2→38.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9847 0 184 138 10169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005710178
X-RAY DIFFRACTIONf_angle_d0.813813873
X-RAY DIFFRACTIONf_chiral_restr0.05021663
X-RAY DIFFRACTIONf_plane_restr0.00521819
X-RAY DIFFRACTIONf_dihedral_angle_d11.05746203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.2996260.31135X-RAY DIFFRACTION11.62
2.05-2.110.3863400.31751236X-RAY DIFFRACTION12.56
2.11-2.180.3291510.35321330X-RAY DIFFRACTION13.88
2.18-2.260.3917570.36791535X-RAY DIFFRACTION15.8
2.26-2.350.4229550.36511750X-RAY DIFFRACTION17.87
2.35-2.460.3572760.37412117X-RAY DIFFRACTION21.85
2.46-2.590.4209710.36512591X-RAY DIFFRACTION26.41
2.59-2.750.40881190.36153373X-RAY DIFFRACTION34.61
2.75-2.960.37841390.33184795X-RAY DIFFRACTION48.54
2.96-3.260.34322580.29418400X-RAY DIFFRACTION84.64
3.26-3.730.32412950.2499548X-RAY DIFFRACTION97
3.73-4.70.25163100.20089906X-RAY DIFFRACTION98.86
4.7-38.270.23143040.21489930X-RAY DIFFRACTION96.64
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)
11.53426530119-0.3347480810511.299971588980.181386931216-0.5808669588162.033114191830.01445425169010.205987151755-0.02939390415260.0100758567121-0.0988981669744-0.1179127610790.04138697185540.1917985511940.01962333550150.35582693708-0.165398178161-0.06056800394581.138141159660.2654027025580.401306248111226.52213294112.709071034574.1048220781
21.353042418810.2038073870240.9907301949070.311994228120.2281006351371.331758398180.00954931948558-0.276973781569-0.02050133591180.0681819293491-0.125595665151-0.0274911847222-0.0801280248379-0.1098625045820.09746276030370.2111121629090.02604310609090.0397483534636-0.0208808306454-0.009186543918390.115355857507154.4697097296.3964864503114.6585558116
31.417210370430.335545110240.6954519095190.2103528251320.2208341609920.4105546109480.0379936204564-0.234009540816-0.1849589849950.06532863163920.07147305796510.1020363542610.0440506461217-0.0898483375808-0.01728676044890.2458992433170.0131425676416-0.1223039119761.01144377252-0.008806709999960.55706031651672.1624717097-11.333817934-34.1987172526
40.3035037950550.007467895005710.2602597181460.3486113147980.01570792376340.492837649586-0.02421562499520.284498146493-0.140833368339-0.3276823582080.004460069337910.1241811572090.121137635004-0.0208411661457-0.03526597836020.53508520147-0.16680602045-0.13018278771.55674513602-0.01381259563570.81732307429541.0126776388-17.563612766-68.1413875114
50.848883830748-0.1976192451470.696230845050.343855415787-0.1427106397810.628689100425-0.272554707575-0.2726959188460.04758079728670.295326939480.03527217709420.0551824859544-0.238987604742-0.414532847768-0.07161223323990.7243713491090.54760617059-0.1342836573131.17015706342-0.2335666420980.36100737566126.11508109812.938840365318.4152594508
61.47823418711-0.2859076889861.469597090220.223073684377-0.2162139224521.66395916567-0.1027028916660.046075508437-0.0676678141178-0.1939120615440.02673274274360.000452057745154-0.105951410272-0.08726856912410.03973462614270.3426881014380.0256454573646-0.01854351583230.119857054887-0.04878258135760.334318528145180.5514615691.1683826596763.3945693473
71.40227206238-0.1052748205960.7737363707880.0574435599995-0.2872675121641.671233048950.089843293680.0826641559985-0.1191749903920.0805071821146-0.0880379805975-0.04091415179260.01859742221080.6374758954310.01262345380120.2153448310310.035980751218-0.04066625530090.268593607999-0.01102372997670.407171699902225.409598749-1.0296388758495.5900613459
81.97001891547-0.03515163436480.8019808280480.2423968346070.1110701114270.47443134031-0.0173690604152-0.194831655165-0.131290659990.078004711344-0.0296776289956-0.137751389747-0.032260461453-0.007004333418240.0007799093194760.359752543883-0.0313421027379-0.1495614062791.31713917530.2283811558940.799508666682270.411107125-13.7348707736111.039795174
90.189463046829-0.0915805335118-0.02015821702120.374165249385-0.1471119008150.6130381056010.0760766769954-0.195310097132-0.1103029138660.2852855275280.131343502824-0.1195409181060.136405829805-0.0520523106614-0.09197611005831.093894016240.0210251258299-0.2227180655011.775420624220.3429643342691.32005883414301.013259342-21.942662003144.033122274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 1:94
2X-RAY DIFFRACTION2chain A and resid 95:428
3X-RAY DIFFRACTION3chain A and resid 429:525
4X-RAY DIFFRACTION4chain A and resid 526:642
5X-RAY DIFFRACTION5chain B and resid 1:200
6X-RAY DIFFRACTION6chain B and resid 201:318
7X-RAY DIFFRACTION7chain B and resid 319:438
8X-RAY DIFFRACTION8chain B and resid 439:544
9X-RAY DIFFRACTION9chain B and resid 545:641

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