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- PDB-6vfw: Crystal structure of human delta protocadherin 10 EC1-EC4 -

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Basic information

Entry
Database: PDB / ID: 6vfw
TitleCrystal structure of human delta protocadherin 10 EC1-EC4
ComponentsProtocadherin-10
KeywordsCELL ADHESION / cadherin extracellular region / non-clustered delta2 family / protocadherin / homophilic adhesion/recognition calcium-dependent / adhesion molecule
Function / homology
Function and homology information


homophilic cell adhesion via plasma membrane adhesion molecules / nervous system development / cell adhesion / calcium ion binding / plasma membrane
Similarity search - Function
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, 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-10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsHarrison, O.J. / Brasch, J. / Shapiro, L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01MH114817 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM118584 United States
National Science Foundation (NSF, United States)MCB-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 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / 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_validate_close_contact / refine_hist / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _refine_hist.d_res_high / _refine_hist.d_res_low / _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 11, 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 / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protocadherin-10
B: Protocadherin-10
C: Protocadherin-10
D: Protocadherin-10
E: Protocadherin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,44065
Polymers241,5505
Non-polymers8,89060
Water41423
1
A: Protocadherin-10
C: Protocadherin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,17626
Polymers96,6202
Non-polymers3,55624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-60 kcal/mol
Surface area45990 Å2
MethodPISA
2
B: Protocadherin-10
D: Protocadherin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,17626
Polymers96,6202
Non-polymers3,55624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-60 kcal/mol
Surface area45630 Å2
MethodPISA
3
E: Protocadherin-10
hetero molecules

E: Protocadherin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,17626
Polymers96,6202
Non-polymers3,55624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7240 Å2
ΔGint-56 kcal/mol
Surface area45260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)346.550, 73.193, 246.328
Angle α, β, γ (deg.)90.000, 132.057, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNPROPRO(chain A and (resseq 2:106 or (resid 107 and (name...AA2 - 1202 - 120
12PHEPHELEULEU(chain A and (resseq 2:106 or (resid 107 and (name...AA124 - 139124 - 139
13ASPASPTYRTYR(chain A and (resseq 2:106 or (resid 107 and (name...AA141 - 142141 - 142
14ILEILEVALVAL(chain A and (resseq 2:106 or (resid 107 and (name...AA144 - 154144 - 154
15THRTHRTHRTHR(chain A and (resseq 2:106 or (resid 107 and (name...AA156156
16GLYGLYASNASN(chain A and (resseq 2:106 or (resid 107 and (name...AA160 - 161160 - 161
17PHEPHELEULEU(chain A and (resseq 2:106 or (resid 107 and (name...AA163 - 168163 - 168
18LYSLYSGLUGLU(chain A and (resseq 2:106 or (resid 107 and (name...AA170 - 175170 - 175
19GLNGLNHISHIS(chain A and (resseq 2:106 or (resid 107 and (name...AA177 - 180177 - 180
110TYRTYRASPASP(chain A and (resseq 2:106 or (resid 107 and (name...AA182 - 188182 - 188
111PROPROVALVAL(chain A and (resseq 2:106 or (resid 107 and (name...AA209 - 269209 - 269
112SERSERSERSER(chain A and (resseq 2:106 or (resid 107 and (name...AA271 - 273271 - 273
113ILEILEALAALA(chain A and (resseq 2:106 or (resid 107 and (name...AA276 - 280276 - 280
114GLUGLUPROPRO(chain A and (resseq 2:106 or (resid 107 and (name...AA282 - 288282 - 288
115THRTHRVALVAL(chain A and (resseq 2:106 or (resid 107 and (name...AA290 - 306290 - 306
116VALVALVALVAL(chain A and (resseq 2:106 or (resid 107 and (name...AA309 - 329309 - 329
117VALVALLYSLYS(chain A and (resseq 2:106 or (resid 107 and (name...AA331 - 347331 - 347
118ALAALASERSER(chain A and (resseq 2:106 or (resid 107 and (name...AA349 - 351349 - 351
119GLYGLYALAALA(chain A and (resseq 2:106 or (resid 107 and (name...AA353 - 361353 - 361
120PHEPHEASPASP(chain A and (resseq 2:106 or (resid 107 and (name...AA363 - 367363 - 367
121ASPASPSERSER(chain A and (resseq 2:106 or (resid 107 and (name...AA369 - 370369 - 370
122ASNASNLEULEU(chain A and (resseq 2:106 or (resid 107 and (name...AA373 - 380373 - 380
123VALVALPHEPHE(chain A and (resseq 2:106 or (resid 107 and (name...AA384 - 386384 - 386
124SERSERSERSER(chain A and (resseq 2:106 or (resid 107 and (name...AA390 - 391390 - 391
125ASNASNPROPRO(chain A and (resseq 2:106 or (resid 107 and (name...AA394 - 403394 - 403
126ASPASPASPASP(chain A and (resseq 2:106 or (resid 107 and (name...AA405405
127GLUGLUSERSER(chain A and (resseq 2:106 or (resid 107 and (name...AA407 - 411407 - 411
128LEULEUALAALA(chain A and (resseq 2:106 or (resid 107 and (name...AA414 - 418414 - 418
129ASPASPASPASP(chain A and (resseq 2:106 or (resid 107 and (name...AA420420
130GLYGLYSERSER(chain A and (resseq 2:106 or (resid 107 and (name...AA422 - 429422 - 429
131SERSERVALVAL(chain A and (resseq 2:106 or (resid 107 and (name...AA431 - 434431 - 434
132VALVALASPASP(chain A and (resseq 2:106 or (resid 107 and (name...AA436 - 438436 - 438
133HOHHOHHOHHOH(chain A and (resseq 2:106 or (resid 107 and (name...ANB601 - 603
21GLNGLNPROPRO(chain B and (resseq 2:106 or (resid 107 and (name...BB2 - 1202 - 120
22PHEPHELEULEU(chain B and (resseq 2:106 or (resid 107 and (name...BB124 - 139124 - 139
23ASPASPTYRTYR(chain B and (resseq 2:106 or (resid 107 and (name...BB141 - 142141 - 142
24ILEILEVALVAL(chain B and (resseq 2:106 or (resid 107 and (name...BB144 - 154144 - 154
25THRTHRTHRTHR(chain B and (resseq 2:106 or (resid 107 and (name...BB156156
26GLYGLYASNASN(chain B and (resseq 2:106 or (resid 107 and (name...BB160 - 161160 - 161
27PHEPHELEULEU(chain B and (resseq 2:106 or (resid 107 and (name...BB163 - 168163 - 168
28LYSLYSGLUGLU(chain B and (resseq 2:106 or (resid 107 and (name...BB170 - 175170 - 175
29GLNGLNHISHIS(chain B and (resseq 2:106 or (resid 107 and (name...BB177 - 180177 - 180
210TYRTYRASPASP(chain B and (resseq 2:106 or (resid 107 and (name...BB182 - 188182 - 188
211PROPROVALVAL(chain B and (resseq 2:106 or (resid 107 and (name...BB209 - 269209 - 269
212SERSERSERSER(chain B and (resseq 2:106 or (resid 107 and (name...BB271 - 273271 - 273
213ILEILEALAALA(chain B and (resseq 2:106 or (resid 107 and (name...BB276 - 280276 - 280
214GLUGLUPROPRO(chain B and (resseq 2:106 or (resid 107 and (name...BB282 - 288282 - 288
215THRTHRVALVAL(chain B and (resseq 2:106 or (resid 107 and (name...BB290 - 306290 - 306
216VALVALVALVAL(chain B and (resseq 2:106 or (resid 107 and (name...BB309 - 329309 - 329
217VALVALLYSLYS(chain B and (resseq 2:106 or (resid 107 and (name...BB331 - 347331 - 347
218ALAALASERSER(chain B and (resseq 2:106 or (resid 107 and (name...BB349 - 351349 - 351
219GLYGLYALAALA(chain B and (resseq 2:106 or (resid 107 and (name...BB353 - 361353 - 361
220PHEPHEASPASP(chain B and (resseq 2:106 or (resid 107 and (name...BB363 - 367363 - 367
221ASPASPSERSER(chain B and (resseq 2:106 or (resid 107 and (name...BB369 - 370369 - 370
222ASNASNLEULEU(chain B and (resseq 2:106 or (resid 107 and (name...BB373 - 380373 - 380
223VALVALPHEPHE(chain B and (resseq 2:106 or (resid 107 and (name...BB384 - 386384 - 386
224SERSERSERSER(chain B and (resseq 2:106 or (resid 107 and (name...BB390 - 391390 - 391
225ASNASNPROPRO(chain B and (resseq 2:106 or (resid 107 and (name...BB394 - 403394 - 403
226ASPASPASPASP(chain B and (resseq 2:106 or (resid 107 and (name...BB405405
227GLUGLUSERSER(chain B and (resseq 2:106 or (resid 107 and (name...BB407 - 411407 - 411
228LEULEUALAALA(chain B and (resseq 2:106 or (resid 107 and (name...BB414 - 418414 - 418
229ASPASPASPASP(chain B and (resseq 2:106 or (resid 107 and (name...BB420420
230GLYGLYSERSER(chain B and (resseq 2:106 or (resid 107 and (name...BB422 - 429422 - 429
231SERSERVALVAL(chain B and (resseq 2:106 or (resid 107 and (name...BB431 - 434431 - 434
232VALVALASPASP(chain B and (resseq 2:106 or (resid 107 and (name...BB436 - 438436 - 438
233HOHHOHHOHHOH(chain B and (resseq 2:106 or (resid 107 and (name...BOB601 - 603
31GLNGLNPROPRO(chain C and (resseq 2:106 or (resid 107 and (name...CC2 - 1202 - 120
32PHEPHELEULEU(chain C and (resseq 2:106 or (resid 107 and (name...CC124 - 139124 - 139
33ASPASPTYRTYR(chain C and (resseq 2:106 or (resid 107 and (name...CC141 - 142141 - 142
34ILEILEVALVAL(chain C and (resseq 2:106 or (resid 107 and (name...CC144 - 154144 - 154
35THRTHRTHRTHR(chain C and (resseq 2:106 or (resid 107 and (name...CC156156
36GLYGLYASNASN(chain C and (resseq 2:106 or (resid 107 and (name...CC160 - 161160 - 161
37PHEPHELEULEU(chain C and (resseq 2:106 or (resid 107 and (name...CC163 - 168163 - 168
38LYSLYSGLUGLU(chain C and (resseq 2:106 or (resid 107 and (name...CC170 - 175170 - 175
39GLNGLNHISHIS(chain C and (resseq 2:106 or (resid 107 and (name...CC177 - 180177 - 180
310TYRTYRASPASP(chain C and (resseq 2:106 or (resid 107 and (name...CC182 - 188182 - 188
311PROPROVALVAL(chain C and (resseq 2:106 or (resid 107 and (name...CC209 - 269209 - 269
312SERSERSERSER(chain C and (resseq 2:106 or (resid 107 and (name...CC271 - 273271 - 273
313ILEILEALAALA(chain C and (resseq 2:106 or (resid 107 and (name...CC276 - 280276 - 280
314GLUGLUPROPRO(chain C and (resseq 2:106 or (resid 107 and (name...CC282 - 288282 - 288
315THRTHRVALVAL(chain C and (resseq 2:106 or (resid 107 and (name...CC290 - 306290 - 306
316VALVALVALVAL(chain C and (resseq 2:106 or (resid 107 and (name...CC309 - 329309 - 329
317VALVALLYSLYS(chain C and (resseq 2:106 or (resid 107 and (name...CC331 - 347331 - 347
318ALAALASERSER(chain C and (resseq 2:106 or (resid 107 and (name...CC349 - 351349 - 351
319GLYGLYALAALA(chain C and (resseq 2:106 or (resid 107 and (name...CC353 - 361353 - 361
320PHEPHEASPASP(chain C and (resseq 2:106 or (resid 107 and (name...CC363 - 367363 - 367
321ASPASPSERSER(chain C and (resseq 2:106 or (resid 107 and (name...CC369 - 370369 - 370
322ASNASNLEULEU(chain C and (resseq 2:106 or (resid 107 and (name...CC373 - 380373 - 380
323VALVALPHEPHE(chain C and (resseq 2:106 or (resid 107 and (name...CC384 - 386384 - 386
324SERSERSERSER(chain C and (resseq 2:106 or (resid 107 and (name...CC390 - 391390 - 391
325ASNASNPROPRO(chain C and (resseq 2:106 or (resid 107 and (name...CC394 - 403394 - 403
326ASPASPASPASP(chain C and (resseq 2:106 or (resid 107 and (name...CC405405
327GLUGLUSERSER(chain C and (resseq 2:106 or (resid 107 and (name...CC407 - 411407 - 411
328LEULEUALAALA(chain C and (resseq 2:106 or (resid 107 and (name...CC414 - 418414 - 418
329ASPASPASPASP(chain C and (resseq 2:106 or (resid 107 and (name...CC420420
330GLYGLYSERSER(chain C and (resseq 2:106 or (resid 107 and (name...CC422 - 429422 - 429
331SERSERVALVAL(chain C and (resseq 2:106 or (resid 107 and (name...CC431 - 434431 - 434
332VALVALASPASP(chain C and (resseq 2:106 or (resid 107 and (name...CC436 - 438436 - 438
333HOHHOHHOHHOH(chain C and (resseq 2:106 or (resid 107 and (name...CPB601 - 603
41GLNGLNPROPRO(chain D and (resseq 2:106 or (resid 107 and (name...DD2 - 1202 - 120
42PHEPHELEULEU(chain D and (resseq 2:106 or (resid 107 and (name...DD124 - 139124 - 139
43ASPASPTYRTYR(chain D and (resseq 2:106 or (resid 107 and (name...DD141 - 142141 - 142
44ILEILEVALVAL(chain D and (resseq 2:106 or (resid 107 and (name...DD144 - 154144 - 154
45THRTHRTHRTHR(chain D and (resseq 2:106 or (resid 107 and (name...DD156156
46GLYGLYASNASN(chain D and (resseq 2:106 or (resid 107 and (name...DD160 - 161160 - 161
47PHEPHELEULEU(chain D and (resseq 2:106 or (resid 107 and (name...DD163 - 168163 - 168
48LYSLYSGLUGLU(chain D and (resseq 2:106 or (resid 107 and (name...DD170 - 175170 - 175
49GLNGLNHISHIS(chain D and (resseq 2:106 or (resid 107 and (name...DD177 - 180177 - 180
410TYRTYRASPASP(chain D and (resseq 2:106 or (resid 107 and (name...DD182 - 188182 - 188
411PROPROVALVAL(chain D and (resseq 2:106 or (resid 107 and (name...DD209 - 269209 - 269
412SERSERSERSER(chain D and (resseq 2:106 or (resid 107 and (name...DD271 - 273271 - 273
413ILEILEALAALA(chain D and (resseq 2:106 or (resid 107 and (name...DD276 - 280276 - 280
414GLUGLUPROPRO(chain D and (resseq 2:106 or (resid 107 and (name...DD282 - 288282 - 288
415THRTHRVALVAL(chain D and (resseq 2:106 or (resid 107 and (name...DD290 - 306290 - 306
416VALVALVALVAL(chain D and (resseq 2:106 or (resid 107 and (name...DD309 - 329309 - 329
417VALVALLYSLYS(chain D and (resseq 2:106 or (resid 107 and (name...DD331 - 347331 - 347
418ALAALASERSER(chain D and (resseq 2:106 or (resid 107 and (name...DD349 - 351349 - 351
419GLYGLYALAALA(chain D and (resseq 2:106 or (resid 107 and (name...DD353 - 361353 - 361
420PHEPHEASPASP(chain D and (resseq 2:106 or (resid 107 and (name...DD363 - 367363 - 367
421ASPASPSERSER(chain D and (resseq 2:106 or (resid 107 and (name...DD369 - 370369 - 370
422ASNASNLEULEU(chain D and (resseq 2:106 or (resid 107 and (name...DD373 - 380373 - 380
423VALVALPHEPHE(chain D and (resseq 2:106 or (resid 107 and (name...DD384 - 386384 - 386
424SERSERSERSER(chain D and (resseq 2:106 or (resid 107 and (name...DD390 - 391390 - 391
425ASNASNPROPRO(chain D and (resseq 2:106 or (resid 107 and (name...DD394 - 403394 - 403
426ASPASPASPASP(chain D and (resseq 2:106 or (resid 107 and (name...DD405405
427GLUGLUSERSER(chain D and (resseq 2:106 or (resid 107 and (name...DD407 - 411407 - 411
428LEULEUALAALA(chain D and (resseq 2:106 or (resid 107 and (name...DD414 - 418414 - 418
429ASPASPASPASP(chain D and (resseq 2:106 or (resid 107 and (name...DD420420
430GLYGLYSERSER(chain D and (resseq 2:106 or (resid 107 and (name...DD422 - 429422 - 429
431SERSERVALVAL(chain D and (resseq 2:106 or (resid 107 and (name...DD431 - 434431 - 434
432VALVALASPASP(chain D and (resseq 2:106 or (resid 107 and (name...DD436 - 438436 - 438
433HOHHOHHOHHOH(chain D and (resseq 2:106 or (resid 107 and (name...DQB601 - 603
51GLNGLNPROPRO(chain E and (resseq 2:106 or (resid 107 and (name...EE2 - 1202 - 120
52PHEPHELEULEU(chain E and (resseq 2:106 or (resid 107 and (name...EE124 - 139124 - 139
53ASPASPTYRTYR(chain E and (resseq 2:106 or (resid 107 and (name...EE141 - 142141 - 142
54ILEILEVALVAL(chain E and (resseq 2:106 or (resid 107 and (name...EE144 - 154144 - 154
55THRTHRTHRTHR(chain E and (resseq 2:106 or (resid 107 and (name...EE156156
56GLYGLYASNASN(chain E and (resseq 2:106 or (resid 107 and (name...EE160 - 161160 - 161
57PHEPHELEULEU(chain E and (resseq 2:106 or (resid 107 and (name...EE163 - 168163 - 168
58LYSLYSGLUGLU(chain E and (resseq 2:106 or (resid 107 and (name...EE170 - 175170 - 175
59GLNGLNHISHIS(chain E and (resseq 2:106 or (resid 107 and (name...EE177 - 180177 - 180
510TYRTYRASPASP(chain E and (resseq 2:106 or (resid 107 and (name...EE182 - 188182 - 188
511PROPROVALVAL(chain E and (resseq 2:106 or (resid 107 and (name...EE209 - 269209 - 269
512SERSERSERSER(chain E and (resseq 2:106 or (resid 107 and (name...EE271 - 273271 - 273
513ILEILEALAALA(chain E and (resseq 2:106 or (resid 107 and (name...EE276 - 280276 - 280
514GLUGLUPROPRO(chain E and (resseq 2:106 or (resid 107 and (name...EE282 - 288282 - 288
515THRTHRVALVAL(chain E and (resseq 2:106 or (resid 107 and (name...EE290 - 306290 - 306
516VALVALVALVAL(chain E and (resseq 2:106 or (resid 107 and (name...EE309 - 329309 - 329
517VALVALLYSLYS(chain E and (resseq 2:106 or (resid 107 and (name...EE331 - 347331 - 347
518ALAALASERSER(chain E and (resseq 2:106 or (resid 107 and (name...EE349 - 351349 - 351
519GLYGLYALAALA(chain E and (resseq 2:106 or (resid 107 and (name...EE353 - 361353 - 361
520PHEPHEASPASP(chain E and (resseq 2:106 or (resid 107 and (name...EE363 - 367363 - 367
521ASPASPSERSER(chain E and (resseq 2:106 or (resid 107 and (name...EE369 - 370369 - 370
522ASNASNLEULEU(chain E and (resseq 2:106 or (resid 107 and (name...EE373 - 380373 - 380
523VALVALPHEPHE(chain E and (resseq 2:106 or (resid 107 and (name...EE384 - 386384 - 386
524SERSERSERSER(chain E and (resseq 2:106 or (resid 107 and (name...EE390 - 391390 - 391
525ASNASNPROPRO(chain E and (resseq 2:106 or (resid 107 and (name...EE394 - 403394 - 403
526ASPASPASPASP(chain E and (resseq 2:106 or (resid 107 and (name...EE405405
527GLUGLUSERSER(chain E and (resseq 2:106 or (resid 107 and (name...EE407 - 411407 - 411
528LEULEUALAALA(chain E and (resseq 2:106 or (resid 107 and (name...EE414 - 418414 - 418
529ASPASPASPASP(chain E and (resseq 2:106 or (resid 107 and (name...EE420420
530GLYGLYSERSER(chain E and (resseq 2:106 or (resid 107 and (name...EE422 - 429422 - 429
531SERSERVALVAL(chain E and (resseq 2:106 or (resid 107 and (name...EE431 - 434431 - 434
532VALVALASPASP(chain E and (resseq 2:106 or (resid 107 and (name...EE436 - 438436 - 438
533HOHHOHHOHHOH(chain E and (resseq 2:106 or (resid 107 and (name...ERB601 - 603

-
Components

#1: Protein
Protocadherin-10 /


Mass: 48309.922 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCDH10, KIAA1400 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9P2E7
#2: Polysaccharide
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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: 1056.964 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 45
Source method: isolated from a genetically manipulated source
Formula: Ca
#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.: 10
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.87 Å3/Da / Density % sol: 74.73 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 12% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.1M Tris-bicine buffer pH8.5, 10% 0.02 M D-glucose, 0.02 M D-mannose, 0.02 M D-galactose, 0.02 M L-fucose, 0.02 M D-xylose, 0.02 M N-acetyl-D- ...Details: 12% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.1M Tris-bicine buffer pH8.5, 10% 0.02 M D-glucose, 0.02 M D-mannose, 0.02 M D-galactose, 0.02 M L-fucose, 0.02 M D-xylose, 0.02 M N-acetyl-D-glucosamine with no further cryoprotection

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.6→40 Å / Num. obs: 52814 / % possible obs: 98.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 152.358254998 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.123 / Rrim(I) all: 0.146 / Net I/σ(I): 5.4
Reflection shellResolution: 3.6→3.71 Å / Redundancy: 3.6 % / Rmerge(I) obs: 4.649 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 4543 / CC1/2: 0.29 / Rrim(I) all: 5.476 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VFQ

6vfq


Resolution: 3.6→19.99 Å / SU ML: 0.6222 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 42.15
RfactorNum. reflection% reflectionSelection details
Rfree0.2948 1880 3.75 %Random
Rwork0.2766 ---
obs0.2773 50086 93.37 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 270.8 Å2
Refinement stepCycle: LAST / Resolution: 3.6→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16399 0 510 23 16932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012478438961117527
X-RAY DIFFRACTIONf_angle_d0.78269171437723596
X-RAY DIFFRACTIONf_chiral_restr0.04964242113912810
X-RAY DIFFRACTIONf_plane_restr0.003613858570063109
X-RAY DIFFRACTIONf_dihedral_angle_d13.962112499610551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.69680.5498810.55012083X-RAY DIFFRACTION52.5753158406
3.6968-3.80490.5681857754281210.5346697488123690X-RAY DIFFRACTION92.9738960722
3.8049-3.92680.4983634596041590.4775790128023694X-RAY DIFFRACTION95.3005194163
3.9268-4.0660.4530733533681450.4278505563113842X-RAY DIFFRACTION96.490803485
4.066-4.22730.4035289730471400.3876080373953776X-RAY DIFFRACTION96.3345633456
4.2273-4.41770.367775462211670.331514828873813X-RAY DIFFRACTION97.525116393
4.4177-4.64790.3355317314371350.301192595483929X-RAY DIFFRACTION98.0694980695
4.6479-4.9350.2692471948621600.2709019826273842X-RAY DIFFRACTION97.514619883
4.935-5.30940.2903742936371410.2779722228193859X-RAY DIFFRACTION97.3709834469
5.3094-5.83160.2919603909951440.2817371444273879X-RAY DIFFRACTION97.3620522749
5.8316-6.64810.3171832971571800.2832113522193942X-RAY DIFFRACTION98.6124401914
6.6481-8.27580.3259776627471040.2497020944143910X-RAY DIFFRACTION96.6064981949
8.2758-19.9853140970.2021201041922030.1783459760683947X-RAY DIFFRACTION96.9399672974
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)
10.2447132832210.1534933155950.0670144425990.08963766580650.03566319342310.007988823297660.3516348835960.200977532194-1.389405690430.615884015608-0.37493308768-0.9572806123620.2354412502320.300822426463-9.95878348762E-52.80988955706-0.283353365499-0.1466363544655.669162948320.6668441426953.74103149443161.97944283419.300205638881.34453244
20.016183158299-0.0570358636084-0.07135067069590.1258140447230.2001302866760.2434672581490.763295700819-0.117999013550.0279181069047-0.9366457491940.05374373874060.7443935266060.22206887865-0.9638528195530.0001369801405412.89624194036-0.446184599135-0.4762851991174.382838719110.9528530831544.48895733219-19.364415076312.003067931633.3870920293
34.18160262696-0.4205485403720.7159428524180.23764638101-0.2167793405310.6296862844490.1753664211590.165075827487-1.94566799296-0.248530454829-0.01582421872790.166030164486-0.01642995155470.041385970479-0.0008160853969852.56756353544-0.2642875893480.01844481206472.14587653356-0.09449654656012.6750655481983.47286237425.7050853893135.6667945355
44.395023590170.815882841560.5961453411810.3406734926510.1356710293390.643882929667-0.3731579733310.45916439322-0.121142092231-0.07993175156510.316032002162-0.2324764042840.07697891745160.1110434962980.0005036475068832.48173767198-0.2965516704250.1344163595112.38954642802-0.2102791278562.3703019766443.8188923958-11.575069242750.6968486454
54.36998794248-0.08558623082521.524358810120.4754139295760.03230101911761.0364358417-0.406443849276-0.3404597877740.847724687544-0.04165977266090.004776072645370.22446403456-0.376868786182-0.5953171983840.00382465336482.736075697760.00267275091907-0.1375435612.0735504652-0.1862589251122.48214974687-0.971222491361-21.208500831811.415110123
65.60158568318-0.5860059951592.137115398520.466162259481-0.4025138085542.13119890811-0.24896001187-0.1632714647280.0645467782671-0.02636415333780.154549108204-0.0124723796618-0.1505072222890.170428537407-0.003149452197392.44643520982-0.1924168118850.1062143951091.650571994130.003708482362622.0646956162876.639559443822.253495785948.2095661116
74.655512325660.1695476423812.578270051590.181061366243-0.09981011879971.96268687448-0.00495250850823-0.3740733800040.311016806389-0.0766314334628-0.06399454480420.07858950668130.121469100334-0.1229148398860.01220664895242.45219430081-0.1611738959690.07149303373642.18530737709-0.02614924288091.9415508944965.88816418158.935545753566.2971779859
81.31290810993-0.463260800959-0.5404052602923.22461461861-1.246997975073.072302241120.0258906914231-0.857839292855-2.129838122930.1346476843010.0711257713454-0.7438909933810.186805189013-0.0371777168012-0.006831915203182.45317075597-0.05835242012830.09845101703232.38443809390.4754137621412.6006524871176.31864008310.537534381461.2095561059
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 1:96
2X-RAY DIFFRACTION2chain B and resid 1:98
3X-RAY DIFFRACTION3chain C and resid 1:334
4X-RAY DIFFRACTION4chain D and not hetero
5X-RAY DIFFRACTION5chain E and not hetero
6X-RAY DIFFRACTION6chain A and resid 97:450
7X-RAY DIFFRACTION7chain B and resid 99:450
8X-RAY DIFFRACTION8chain c and resid 335:450

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