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

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基本情報

登録情報
データベース: PDB / ID: 6vfw
タイトルCrystal structure of human delta protocadherin 10 EC1-EC4
要素Protocadherin-10
キーワードCELL ADHESION / cadherin extracellular region / non-clustered delta2 family / protocadherin / homophilic adhesion/recognition calcium-dependent / adhesion molecule
機能・相同性
機能・相同性情報


homophilic cell adhesion via plasma membrane adhesion molecules / nervous system development / postsynaptic membrane / cell adhesion / calcium ion binding / glutamatergic synapse / plasma membrane
類似検索 - 分子機能
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 ...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 / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
alpha-D-mannopyranose / Protocadherin-10
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.6 Å
データ登録者Harrison, O.J. / Brasch, J. / Shapiro, L.
資金援助 米国, 3件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01MH114817 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM118584 米国
National Science Foundation (NSF, United States)MCB-1412472 米国
引用ジャーナル: Cell Rep / 年: 2020
タイトル: Family-wide Structural and Biophysical Analysis of Binding Interactions among Non-clustered δ-Protocadherins.
著者: 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 /
要旨: 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.
履歴
登録2020年1月6日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年3月11日Provider: repository / タイプ: Initial release
改定 2.02020年7月29日Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
カテゴリ: 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
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12023年10月11日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
カテゴリ: 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
改定 2.22024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Protocadherin-10
B: Protocadherin-10
C: Protocadherin-10
D: Protocadherin-10
E: Protocadherin-10
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)250,44065
ポリマ－241,5505
非ポリマー8,89060
水41423
1
A: Protocadherin-10
C: Protocadherin-10
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)100,17626
ポリマ－96,6202
非ポリマー3,55624
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-60 kcal/mol
Surface area45990 Å2
手法PISA
2
B: Protocadherin-10
D: Protocadherin-10
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)100,17626
ポリマ－96,6202
非ポリマー3,55624
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-60 kcal/mol
Surface area45630 Å2
手法PISA
3
E: Protocadherin-10
ヘテロ分子

E: Protocadherin-10
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)100,17626
ポリマ－96,6202
非ポリマー3,55624
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7240 Å2
ΔGint-56 kcal/mol
Surface area45260 Å2
手法PISA
単位格子
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
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41
51

NCSドメイン領域:

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

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要素

#1: タンパク質
Protocadherin-10


分子量: 48309.922 Da / 分子数: 5 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PCDH10, KIAA1400 / 細胞株 (発現宿主): HEK293 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q9P2E7
#2: 多糖
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


タイプ: oligosaccharide / 分子量: 1056.964 Da / 分子数: 5 / 由来タイプ: 組換発現
記述子タイププログラム
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: 化合物...
ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 45 / 由来タイプ: 組換発現 / 式: Ca
#4: 糖
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / α-D-マンノピラノ-ス


タイプ: D-saccharide, alpha linking / 分子量: 180.156 Da / 分子数: 10 / 由来タイプ: 組換発現 / 式: C6H12O6
識別子タイププログラム
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: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 23 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかN
Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 4.87 Å3/Da / 溶媒含有率: 74.73 %
結晶化温度: 296 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.5
詳細: 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- ...詳細: 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

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 24-ID-C / 波長: 0.979 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2016年6月29日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.979 Å / 相対比: 1
反射解像度: 3.6→40 Å / Num. obs: 52814 / % possible obs: 98.2 % / 冗長度: 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
反射 シェル解像度: 3.6→3.71 Å / 冗長度: 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

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解析

ソフトウェア
名称バージョン分類
PHENIX1.10.1_2155精密化
XDSデータ削減
Aimlessデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 6VFQ

6vfq


解像度: 3.6→19.99 Å / SU ML: 0.6222 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 42.15
Rfactor反射数%反射Selection details
Rfree0.2948 1880 3.75 %Random
Rwork0.2766 ---
obs0.2773 50086 93.37 %-
溶媒の処理減衰半径: 0.8 Å / VDWプローブ半径: 1 Å
原子変位パラメータBiso mean: 270.8 Å2
精密化ステップサイクル: LAST / 解像度: 3.6→19.99 Å
タンパク質核酸リガンド溶媒全体
原子数16399 0 510 23 16932
拘束条件
Refine-IDタイプDev ideal数
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精密化 シェル
解像度 (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
精密化 TLS

手法: 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
精密化 TLSグループ
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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万見について

-
お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る