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- PDB-5b1b: Bovine heart cytochrome c oxidase in the fully reduced state at 1... -

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基本情報

登録情報
データベース: PDB / ID: 5b1b
タイトルBovine heart cytochrome c oxidase in the fully reduced state at 1.6 angstrom resolution
要素(Cytochrome c oxidase subunit ...) x 13
キーワードOXIDOREDUCTASE / respiratory chain / Proton pump / Heme
機能・相同性
機能・相同性情報


Complex IV assembly / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / Respiratory electron transport / respiratory chain complex IV / respiratory chain complex / cytochrome-c oxidase / oxidative phosphorylation ...Complex IV assembly / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / Respiratory electron transport / respiratory chain complex IV / respiratory chain complex / cytochrome-c oxidase / oxidative phosphorylation / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / Mitochondrial protein degradation / ATP synthesis coupled electron transport / enzyme regulator activity / aerobic respiration / central nervous system development / respiratory electron transport chain / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / metal ion binding
類似検索 - 分子機能
Cytochrome C Oxidase; Chain F / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit VIb / Cytochrome C Oxidase; Chain D / Cytochrome c oxidase subunit IV / Cytochrome C Oxidase; Chain K / Cytochrome C Oxidase, chain K / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit VIIa / Cytochrome C Oxidase; Chain I ...Cytochrome C Oxidase; Chain F / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit VIb / Cytochrome C Oxidase; Chain D / Cytochrome c oxidase subunit IV / Cytochrome C Oxidase; Chain K / Cytochrome C Oxidase, chain K / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit VIIa / Cytochrome C Oxidase; Chain I / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome C Oxidase; Chain G / Cytochrome c oxidase, subunit VIa / Cytochrome C Oxidase; Chain M / Cytochrome C Oxidase; Chain L / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit III, four-helix bundle / Cytochrome C Oxidase; Chain J / Helix Hairpins - #90 / Cytochrome c oxidase, subunit 8 / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit 8 superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / : / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIc / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Cytochrome C oxidase, subunit VIIB domain superfamily / Cytochrome c oxidase, subunit VIIa superfamily / Cytochrome C oxidase chain VIIB / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, subunit VIb / : / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit Va / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase, subunit II / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Helix Hairpins - #70 / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Cupredoxins - blue copper proteins / Cupredoxin / Four Helix Bundle (Hemerythrin (Met), subunit A) / Few Secondary Structures / Irregular / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Helix Hairpins / Alpha Horseshoe / Arc Repressor Mutant, subunit A / Up-down Bundle / Immunoglobulin-like
類似検索 - ドメイン・相同性
CARDIOLIPIN / CHOLIC ACID / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / Chem-PEK / Chem-PGV / PHOSPHATE ION / Chem-PSC / TRISTEAROYLGLYCEROL ...CARDIOLIPIN / CHOLIC ACID / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / Chem-PEK / Chem-PGV / PHOSPHATE ION / Chem-PSC / TRISTEAROYLGLYCEROL / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 6B1 / Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase subunit 6C / Cytochrome c oxidase subunit 7A1, mitochondrial / Cytochrome c oxidase subunit 6A2, mitochondrial / Cytochrome c oxidase subunit 8B, mitochondrial / Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome c oxidase subunit 2
類似検索 - 構成要素
生物種Bos taurus (ウシ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.6 Å
データ登録者Yano, N. / Muramoto, K. / Shimada, A. / Takemura, S. / Baba, J. / Fujisawa, H. / Mochizuki, M. / Shinzawa-Itoh, K. / Yamashita, E. / Tsukihara, T. / Yoshikawa, S.
資金援助 日本, 3件
組織認可番号国
Ministry of Science, Education and Sports of the Republic of Croatia2247012 日本
Japan Society for the Promotion of Science (JSPS)22370060 日本
Japan Society for the Promotion of Science (JSPS)26291033 日本
引用ジャーナル: J.Biol.Chem. / 年: 2016
タイトル: The Mg2+-containing Water Cluster of Mammalian Cytochrome c Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle.
著者: Yano, N. / Muramoto, K. / Shimada, A. / Takemura, S. / Baba, J. / Fujisawa, H. / Mochizuki, M. / Shinzawa-Itoh, K. / Yamashita, E. / Tsukihara, T. / Yoshikawa, S.
履歴
登録2015年12月1日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02016年9月14日Provider: repository / タイプ: Initial release
改定 1.12016年11月23日Group: Database references
改定 1.22020年2月26日Group: Data collection / Database references / Derived calculations
カテゴリ: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
改定 2.02021年10月13日Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_2 / diffrn / entity / entity_poly / entity_poly_seq / entity_src_nat / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns_shell / software / struct / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_sheet_range / struct_site / struct_site_gen
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn.pdbx_serial_crystal_experiment / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_nat.pdbx_end_seq_num / _pdbx_audit_support.funding_organization / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _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.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_starting_model / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _reflns_shell.number_unique_obs / _struct.pdbx_CASP_flag / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
解説: Model completeness
詳細: The previous analysis had not assigned any ethylene glycol molecule used as cry-protectant. Sixty-two ethylene glycol molecules were located in the crystal and multiple structures were ...詳細: The previous analysis had not assigned any ethylene glycol molecule used as cry-protectant. Sixty-two ethylene glycol molecules were located in the crystal and multiple structures were included in the residues from 380 to 385 of subunits A and N.
Provider: author / タイプ: Coordinate replacement
改定 2.12023年11月8日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / pdbx_validate_chiral

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Cytochrome c oxidase subunit 1
B: Cytochrome c oxidase subunit 2
C: Cytochrome c oxidase subunit 3
D: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
E: Cytochrome c oxidase subunit 5A, mitochondrial
F: Cytochrome c oxidase subunit 5B, mitochondrial
G: Cytochrome c oxidase subunit 6A2, mitochondrial
H: Cytochrome c oxidase subunit 6B1
I: Cytochrome c oxidase subunit 6C
J: Cytochrome c oxidase subunit 7A1, mitochondrial
K: Cytochrome c oxidase subunit 7B, mitochondrial
L: Cytochrome c oxidase subunit 7C, mitochondrial
M: Cytochrome c oxidase subunit 8B, mitochondrial
N: Cytochrome c oxidase subunit 1
O: Cytochrome c oxidase subunit 2
P: Cytochrome c oxidase subunit 3
Q: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
R: Cytochrome c oxidase subunit 5A, mitochondrial
S: Cytochrome c oxidase subunit 5B, mitochondrial
T: Cytochrome c oxidase subunit 6A2, mitochondrial
U: Cytochrome c oxidase subunit 6B1
V: Cytochrome c oxidase subunit 6C
W: Cytochrome c oxidase subunit 7A1, mitochondrial
X: Cytochrome c oxidase subunit 7B, mitochondrial
Y: Cytochrome c oxidase subunit 7C, mitochondrial
Z: Cytochrome c oxidase subunit 8B, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)449,063159
ポリマ－404,13326
非ポリマー44,930133
水59,5043303
1
A: Cytochrome c oxidase subunit 1
B: Cytochrome c oxidase subunit 2
C: Cytochrome c oxidase subunit 3
D: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
E: Cytochrome c oxidase subunit 5A, mitochondrial
F: Cytochrome c oxidase subunit 5B, mitochondrial
G: Cytochrome c oxidase subunit 6A2, mitochondrial
H: Cytochrome c oxidase subunit 6B1
I: Cytochrome c oxidase subunit 6C
J: Cytochrome c oxidase subunit 7A1, mitochondrial
K: Cytochrome c oxidase subunit 7B, mitochondrial
L: Cytochrome c oxidase subunit 7C, mitochondrial
M: Cytochrome c oxidase subunit 8B, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)225,54080
ポリマ－202,06713
非ポリマー23,47367
水23413
タイプ名称対称操作数
identity operation1_555x,y,z1
2
N: Cytochrome c oxidase subunit 1
O: Cytochrome c oxidase subunit 2
P: Cytochrome c oxidase subunit 3
Q: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
R: Cytochrome c oxidase subunit 5A, mitochondrial
S: Cytochrome c oxidase subunit 5B, mitochondrial
T: Cytochrome c oxidase subunit 6A2, mitochondrial
U: Cytochrome c oxidase subunit 6B1
V: Cytochrome c oxidase subunit 6C
W: Cytochrome c oxidase subunit 7A1, mitochondrial
X: Cytochrome c oxidase subunit 7B, mitochondrial
Y: Cytochrome c oxidase subunit 7C, mitochondrial
Z: Cytochrome c oxidase subunit 8B, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)223,52379
ポリマ－202,06713
非ポリマー21,45766
水23413
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)181.606, 204.140, 177.653
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
非結晶学的対称性 (NCS)NCS oper:
IDCodeMatrixベクター
1given(1), (1), (1)
2given(-0.992768, -0.004488, 0.119962), (-0.000227, -0.999229, -0.039256), (0.120046, -0.039, 0.992002)164.41495, 625.38745, 2.40745
3given(1), (1), (1)
4given(-0.993212, 0.000992, 0.116313), (-0.006027, -0.999059, -0.042943), (0.116161, -0.043353, 0.992284)163.28622, 626.74615, 4.34892
5given(1), (1), (1)
6given(-0.992508, -0.001076, 0.122176), (-0.003842, -0.999192, -0.040011), (0.12212, -0.04018, 0.991702)162.91132, 625.95697, 2.59309
7given(1), (1), (1)
8given(-0.993229, -0.003045, 0.116136), (6.4E-5, -0.999671, -0.025668), (0.116176, -0.025487, 0.992902)164.74612, 623.078, -1.28649
9given(1), (1), (1)
10given(-0.98936, -0.061405, 0.131893), (0.056003, -0.997448, -0.044288), (0.134276, -0.03643, 0.990274)180.11153, 618.70111, 0.23422
11given(1), (1), (1)
12given(-0.993498, -0.004825, 0.113747), (0.001198, -0.999489, -0.031932), (0.113843, -0.031588, 0.992996)166.07048, 623.698, 0.57206
13given(1), (1), (1)
14given(-0.992566, -0.004956, 0.12161), (-7.3E-5, -0.999146, -0.041308), (0.121711, -0.04101, 0.991718)164.1266, 625.80078, 2.87112
15given(1), (1), (1)
16given(-0.991113, 0.005847, 0.132896), (-0.011301, -0.999123, -0.040327), (0.132544, -0.04147, 0.990309)159.00999, 626.87878, 2.05259
17given(1), (1), (1)
18given(-0.994152, -0.021001, 0.105929), (0.017873, -0.999378, -0.03039), (0.106502, -0.028319, 0.993909)172.45477, 621.41284, 0.33541
19given(1), (1), (1)
20given(-0.993229, 0.001133, 0.11617), (-0.006452, -0.998947, -0.045427), (0.115996, -0.045869, 0.99219)163.64609, 627.29059, 4.84758
21given(1), (1), (1)
22given(-0.993373, 0.006479, 0.114751), (-0.009325, -0.999662, -0.024282), (0.114555, -0.025191, 0.993098)161.88466, 624.284, -1.32942
23given(1), (1), (1)
24given(-0.992644, -0.01651, 0.11994), (0.012597, -0.999366, -0.033314), (0.120414, -0.031558, 0.992222)167.97585, 622.35315, 0.04377
25given(1), (1), (1)
26given(-0.991639, -0.018693, 0.127682), (0.013369, -0.99901, -0.042428), (0.128349, -0.040366, 0.990907)166.92584, 623.85236, 1.60161

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要素

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Cytochrome c oxidase subunit ... , 13種, 26分子 ANBOCPDQERFSGTHUIVJWKXLYMZ

#1: タンパク質 Cytochrome c oxidase subunit 1 / Cytochrome c oxidase polypeptide I


分子量: 57093.852 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P00396, cytochrome-c oxidase
#2: タンパク質 Cytochrome c oxidase subunit 2 / Cytochrome c oxidase polypeptide II


分子量: 26068.404 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P68530, cytochrome-c oxidase
#3: タンパク質 Cytochrome c oxidase subunit 3 / Cytochrome c oxidase polypeptide III


分子量: 29725.328 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P00415, cytochrome-c oxidase
#4: タンパク質 Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase polypeptide IV / Cytochrome c oxidase subunit IV isoform 1 / COX IV-1


分子量: 16913.367 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P00423
#5: タンパク質 Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase polypeptide Va


分子量: 12083.727 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P00426
#6: タンパク質 Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase polypeptide VIa / Cytochrome c oxidase polypeptide Vb


分子量: 10684.038 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P00428
#7: タンパク質 Cytochrome c oxidase subunit 6A2, mitochondrial / Cytochrome c oxidase polypeptide VIa-heart / COXVIAH / Cytochrome c oxidase polypeptide VIb


分子量: 9452.687 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P07471
#8: タンパク質 Cytochrome c oxidase subunit 6B1 / Cytochrome c oxidase polypeptide VII / Cytochrome c oxidase subunit AED / Cytochrome c oxidase ...Cytochrome c oxidase polypeptide VII / Cytochrome c oxidase subunit AED / Cytochrome c oxidase subunit VIb isoform 1 / COX VIb-1


分子量: 9411.600 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P00429
#9: タンパク質 Cytochrome c oxidase subunit 6C / Cytochrome c oxidase polypeptide VIc / Cytochrome c oxidase subunit STA


分子量: 8537.019 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P04038
#10: タンパク質 Cytochrome c oxidase subunit 7A1, mitochondrial / Cytochrome c oxidase subunit VIIIc / VIIIC / Cytochrome c oxidase subunit VIIa-heart / Cytochrome c ...Cytochrome c oxidase subunit VIIIc / VIIIC / Cytochrome c oxidase subunit VIIa-heart / Cytochrome c oxidase subunit VIIa-H / Cytochrome c oxidase subunit VIIa-muscle / Cytochrome c oxidase subunit VIIa-M


分子量: 6553.546 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P07470
#11: タンパク質・ペプチド Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome c oxidase polypeptide VIIb / IHQ


分子量: 5442.168 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P13183
#12: タンパク質・ペプチド Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase polypeptide VIIIA / Cytochrome c oxidase polypeptide VIIc


分子量: 5362.319 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P00430
#13: タンパク質・ペプチド Cytochrome c oxidase subunit 8B, mitochondrial / Cytochrome c oxidase polypeptide VIII-heart / Cytochrome c oxidase subunit 8-1 / Cytochrome c ...Cytochrome c oxidase polypeptide VIII-heart / Cytochrome c oxidase subunit 8-1 / Cytochrome c oxidase subunit 8H / IX / VIIIb


分子量: 4738.523 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P10175

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糖 , 1種, 23分子

#24: 糖...
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE / デシルβ-マルトシド


タイプ: D-saccharide / 分子量: 482.562 Da / 分子数: 23 / 由来タイプ: 組換発現 / 式: C22H42O11 / コメント: 可溶化剤*YM

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非ポリマー , 15種, 3413分子

#14: 化合物
ChemComp-HEA / HEME-A


分子量: 852.837 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C49H56FeN4O6
#15: 化合物 ChemComp-CU / COPPER (II) ION


分子量: 63.546 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Cu
#16: 化合物 ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Mg
#17: 化合物 ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Na
#18: 化合物
ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL


分子量: 749.007 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C40H77O10P / コメント: リン脂質*YM
#19: 化合物
ChemComp-TGL / TRISTEAROYLGLYCEROL / TRIACYLGLYCEROL / トリステアリン


分子量: 891.480 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C57H110O6
#20: 化合物 ChemComp-PSC / (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE / PHOSPHATIDYLCHOLINE / 2-LINOLEOYL-1-PALMITOYL-SN-GYCEROL-3-PHOSPHOCHOLINE


分子量: 759.068 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C42H81NO8P / コメント: リン脂質*YM
#21: 化合物...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 62 / 由来タイプ: 合成 / 式: C2H6O2
#22: 化合物 ChemComp-CUA / DINUCLEAR COPPER ION


分子量: 127.092 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Cu2
#23: 化合物
ChemComp-CHD / CHOLIC ACID / コ-ル酸


分子量: 408.571 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C24H40O5
#25: 化合物
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


分子量: 1464.043 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C81H156O17P2 / コメント: リン脂質*YM
#26: 化合物
ChemComp-PEK / (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE / PHOSPHATIDYLETHANOLAMINE / 2-ARACHIDONOYL-1-STEAROYL-SN-GLYCEROL-3-PHOSPHOETHANOLAMINE


分子量: 768.055 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C43H78NO8P / コメント: リン脂質*YM
#27: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Zn
#28: 化合物 ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 2 / 由来タイプ: 天然 / 式: PO4
#29: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 3303 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかN

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実験情報

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実験

実験手法: X線回折

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試料調製

結晶マシュー密度: 4.01 Å3/Da / 溶媒含有率: 69.36 %
結晶化温度: 277 K / 手法: batch mode / pH: 6.8 / 詳細: PEG 4000, Sodium phosphate, Decylmaltoside

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データ収集

回折平均測定温度: 50 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SPring-8 / ビームライン: BL44XU / 波長: 0.9 Å
検出器タイプ: RAYONIX MX225HE / 検出器: CCD / 日付: 2010年4月23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: 0.9 Å / 相対比: 1
反射解像度: 1.6→200 Å / Num. obs: 850991 / % possible obs: 99.6 % / 冗長度: 6.7 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 25.5
反射 シェル解像度: 1.6→1.62 Å / 冗長度: 5.4 % / Rmerge(I) obs: 0.74 / Num. unique obs: 28158 / % possible all: 99.4

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.13_2998: ???)精密化
DENZOデータ削減
SCALEPACKデータスケーリング
X-PLOR位相決定
精密化構造決定の手法: 分子置換
開始モデル: 2DYR

2dyr


解像度: 1.6→39.897 Å / SU ML: 0.13 / 交差検証法: FREE R-VALUE / σ(F): 2 / 位相誤差: 20.35 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.191 41978 5.02 %RANDOM
Rwork0.1684 ---
obs0.1696 836451 97.49 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 1.6→39.897 Å
タンパク質核酸リガンド溶媒全体
原子数28498 0 2305 3303 34106
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01931928
X-RAY DIFFRACTIONf_angle_d1.62642916
X-RAY DIFFRACTIONf_dihedral_angle_d15.16818620
X-RAY DIFFRACTIONf_chiral_restr0.114527
X-RAY DIFFRACTIONf_plane_restr0.0125100
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61820.271814080.236826295X-RAY DIFFRACTION97
1.6182-1.63720.244213830.223826316X-RAY DIFFRACTION97
1.6372-1.65720.22613920.212826285X-RAY DIFFRACTION98
1.6572-1.67820.234613960.208426371X-RAY DIFFRACTION98
1.6782-1.70020.212514760.199226290X-RAY DIFFRACTION98
1.7002-1.72350.212514130.19426322X-RAY DIFFRACTION98
1.7235-1.74820.219414350.189726260X-RAY DIFFRACTION97
1.7482-1.77430.205113860.180126387X-RAY DIFFRACTION97
1.7743-1.8020.205613530.181426314X-RAY DIFFRACTION97
1.802-1.83150.208313160.180326427X-RAY DIFFRACTION97
1.8315-1.86310.210313680.180926198X-RAY DIFFRACTION97
1.8631-1.8970.212914040.17926233X-RAY DIFFRACTION97
1.897-1.93350.204214460.173926244X-RAY DIFFRACTION97
1.9335-1.97290.204213330.173126370X-RAY DIFFRACTION97
1.9729-2.01580.199413750.169326490X-RAY DIFFRACTION98
2.0158-2.06270.196614350.168526463X-RAY DIFFRACTION98
2.0627-2.11430.195214100.167626444X-RAY DIFFRACTION98
2.1143-2.17150.194814480.16826194X-RAY DIFFRACTION97
2.1715-2.23540.191413820.165426259X-RAY DIFFRACTION97
2.2354-2.30750.184114080.165626135X-RAY DIFFRACTION96
2.3075-2.390.191813170.164126207X-RAY DIFFRACTION96
2.39-2.48560.181113500.1626225X-RAY DIFFRACTION96
2.4856-2.59870.183413490.156526276X-RAY DIFFRACTION97
2.5987-2.73570.183613490.152926573X-RAY DIFFRACTION97
2.7357-2.90710.171914130.155926584X-RAY DIFFRACTION98
2.9071-3.13150.183414390.160326773X-RAY DIFFRACTION98
3.1315-3.44640.186713970.16326984X-RAY DIFFRACTION99
3.4464-3.94480.181514380.158527229X-RAY DIFFRACTION99
3.9448-4.96850.171114550.154227393X-RAY DIFFRACTION99
4.9685-39.8970.204915040.190227932X-RAY DIFFRACTION99
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)
10.26930.0225-0.06650.11530.00340.2970.0010.04150.02120.00540.01360.01840.0162-0.04850.01930.09570.0047-0.00750.07550.00970.08460.977305.95197.999
20.38530.0820.07770.203-0.04650.35560.01410.1247-0.06190.02220.017-0.0782-0.02990.10430.05040.1019-0.0096-0.00040.1164-0.03260.1487126.125312.021194.057
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:514 ) OR ( CHAIN C AND RESID 4:261 ) OR ( CHAIN B AND RESID 1:227 ) OR ( CHAIN E AND RESID 5:109 ) OR ( CHAIN D AND RESID 4:147 ) OR ( CHAIN G AND RESID 1:84 ) OR ( CHAIN F AND RESID 1:98 ) OR ( CHAIN I AND RESID 1:73 ) OR ( CHAIN H AND RESID 7:85 ) OR ( CHAIN K AND RESID 6:54 ) OR ( CHAIN J AND RESID 1:58 ) OR ( CHAIN M AND RESID 1:43 ) OR ( CHAIN L AND RESID 2:47 )A1 - 514
2X-RAY DIFFRACTION1( CHAIN A AND RESID 1:514 ) OR ( CHAIN C AND RESID 4:261 ) OR ( CHAIN B AND RESID 1:227 ) OR ( CHAIN E AND RESID 5:109 ) OR ( CHAIN D AND RESID 4:147 ) OR ( CHAIN G AND RESID 1:84 ) OR ( CHAIN F AND RESID 1:98 ) OR ( CHAIN I AND RESID 1:73 ) OR ( CHAIN H AND RESID 7:85 ) OR ( CHAIN K AND RESID 6:54 ) OR ( CHAIN J AND RESID 1:58 ) OR ( CHAIN M AND RESID 1:43 ) OR ( CHAIN L AND RESID 2:47 )C4 - 261
3X-RAY DIFFRACTION1( CHAIN A AND RESID 1:514 ) OR ( CHAIN C AND RESID 4:261 ) OR ( CHAIN B AND RESID 1:227 ) OR ( CHAIN E AND RESID 5:109 ) OR ( CHAIN D AND RESID 4:147 ) OR ( CHAIN G AND RESID 1:84 ) OR ( CHAIN F AND RESID 1:98 ) OR ( CHAIN I AND RESID 1:73 ) OR ( CHAIN H AND RESID 7:85 ) OR ( CHAIN K AND RESID 6:54 ) OR ( CHAIN J AND RESID 1:58 ) OR ( CHAIN M AND RESID 1:43 ) OR ( CHAIN L AND RESID 2:47 )B1 - 227
4X-RAY DIFFRACTION1( CHAIN A AND RESID 1:514 ) OR ( CHAIN C AND RESID 4:261 ) OR ( CHAIN B AND RESID 1:227 ) OR ( CHAIN E AND RESID 5:109 ) OR ( CHAIN D AND RESID 4:147 ) OR ( CHAIN G AND RESID 1:84 ) OR ( CHAIN F AND RESID 1:98 ) OR ( CHAIN I AND RESID 1:73 ) OR ( CHAIN H AND RESID 7:85 ) OR ( CHAIN K AND RESID 6:54 ) OR ( CHAIN J AND RESID 1:58 ) OR ( CHAIN M AND RESID 1:43 ) OR ( CHAIN L AND RESID 2:47 )E5 - 109
5X-RAY DIFFRACTION1( CHAIN A AND RESID 1:514 ) OR ( CHAIN C AND RESID 4:261 ) OR ( CHAIN B AND RESID 1:227 ) OR ( CHAIN E AND RESID 5:109 ) OR ( CHAIN D AND RESID 4:147 ) OR ( CHAIN G AND RESID 1:84 ) OR ( CHAIN F AND RESID 1:98 ) OR ( CHAIN I AND RESID 1:73 ) OR ( CHAIN H AND RESID 7:85 ) OR ( CHAIN K AND RESID 6:54 ) OR ( CHAIN J AND RESID 1:58 ) OR ( CHAIN M AND RESID 1:43 ) OR ( CHAIN L AND RESID 2:47 )D4 - 147
6X-RAY DIFFRACTION1( CHAIN A AND RESID 1:514 ) OR ( CHAIN C AND RESID 4:261 ) OR ( CHAIN B AND RESID 1:227 ) OR ( CHAIN E AND RESID 5:109 ) OR ( CHAIN D AND RESID 4:147 ) OR ( CHAIN G AND RESID 1:84 ) OR ( CHAIN F AND RESID 1:98 ) OR ( CHAIN I AND RESID 1:73 ) OR ( CHAIN H AND RESID 7:85 ) OR ( CHAIN K AND RESID 6:54 ) OR ( CHAIN J AND RESID 1:58 ) OR ( CHAIN M AND RESID 1:43 ) OR ( CHAIN L AND RESID 2:47 )G1 - 84
7X-RAY DIFFRACTION1( CHAIN A AND RESID 1:514 ) OR ( CHAIN C AND RESID 4:261 ) OR ( CHAIN B AND RESID 1:227 ) OR ( CHAIN E AND RESID 5:109 ) OR ( CHAIN D AND RESID 4:147 ) OR ( CHAIN G AND RESID 1:84 ) OR ( CHAIN F AND RESID 1:98 ) OR ( CHAIN I AND RESID 1:73 ) OR ( CHAIN H AND RESID 7:85 ) OR ( CHAIN K AND RESID 6:54 ) OR ( CHAIN J AND RESID 1:58 ) OR ( CHAIN M AND RESID 1:43 ) OR ( CHAIN L AND RESID 2:47 )F1 - 98
8X-RAY DIFFRACTION1( CHAIN A AND RESID 1:514 ) OR ( CHAIN C AND RESID 4:261 ) OR ( CHAIN B AND RESID 1:227 ) OR ( CHAIN E AND RESID 5:109 ) OR ( CHAIN D AND RESID 4:147 ) OR ( CHAIN G AND RESID 1:84 ) OR ( CHAIN F AND RESID 1:98 ) OR ( CHAIN I AND RESID 1:73 ) OR ( CHAIN H AND RESID 7:85 ) OR ( CHAIN K AND RESID 6:54 ) OR ( CHAIN J AND RESID 1:58 ) OR ( CHAIN M AND RESID 1:43 ) OR ( CHAIN L AND RESID 2:47 )I1 - 73
9X-RAY DIFFRACTION1( CHAIN A AND RESID 1:514 ) OR ( CHAIN C AND RESID 4:261 ) OR ( CHAIN B AND RESID 1:227 ) OR ( CHAIN E AND RESID 5:109 ) OR ( CHAIN D AND RESID 4:147 ) OR ( CHAIN G AND RESID 1:84 ) OR ( CHAIN F AND RESID 1:98 ) OR ( CHAIN I AND RESID 1:73 ) OR ( CHAIN H AND RESID 7:85 ) OR ( CHAIN K AND RESID 6:54 ) OR ( CHAIN J AND RESID 1:58 ) OR ( CHAIN M AND RESID 1:43 ) OR ( CHAIN L AND RESID 2:47 )H7 - 85
10X-RAY DIFFRACTION1( CHAIN A AND RESID 1:514 ) OR ( CHAIN C AND RESID 4:261 ) OR ( CHAIN B AND RESID 1:227 ) OR ( CHAIN E AND RESID 5:109 ) OR ( CHAIN D AND RESID 4:147 ) OR ( CHAIN G AND RESID 1:84 ) OR ( CHAIN F AND RESID 1:98 ) OR ( CHAIN I AND RESID 1:73 ) OR ( CHAIN H AND RESID 7:85 ) OR ( CHAIN K AND RESID 6:54 ) OR ( CHAIN J AND RESID 1:58 ) OR ( CHAIN M AND RESID 1:43 ) OR ( CHAIN L AND RESID 2:47 )K6 - 54
11X-RAY DIFFRACTION1( CHAIN A AND RESID 1:514 ) OR ( CHAIN C AND RESID 4:261 ) OR ( CHAIN B AND RESID 1:227 ) OR ( CHAIN E AND RESID 5:109 ) OR ( CHAIN D AND RESID 4:147 ) OR ( CHAIN G AND RESID 1:84 ) OR ( CHAIN F AND RESID 1:98 ) OR ( CHAIN I AND RESID 1:73 ) OR ( CHAIN H AND RESID 7:85 ) OR ( CHAIN K AND RESID 6:54 ) OR ( CHAIN J AND RESID 1:58 ) OR ( CHAIN M AND RESID 1:43 ) OR ( CHAIN L AND RESID 2:47 )J1 - 58
12X-RAY DIFFRACTION1( CHAIN A AND RESID 1:514 ) OR ( CHAIN C AND RESID 4:261 ) OR ( CHAIN B AND RESID 1:227 ) OR ( CHAIN E AND RESID 5:109 ) OR ( CHAIN D AND RESID 4:147 ) OR ( CHAIN G AND RESID 1:84 ) OR ( CHAIN F AND RESID 1:98 ) OR ( CHAIN I AND RESID 1:73 ) OR ( CHAIN H AND RESID 7:85 ) OR ( CHAIN K AND RESID 6:54 ) OR ( CHAIN J AND RESID 1:58 ) OR ( CHAIN M AND RESID 1:43 ) OR ( CHAIN L AND RESID 2:47 )M1 - 43
13X-RAY DIFFRACTION1( CHAIN A AND RESID 1:514 ) OR ( CHAIN C AND RESID 4:261 ) OR ( CHAIN B AND RESID 1:227 ) OR ( CHAIN E AND RESID 5:109 ) OR ( CHAIN D AND RESID 4:147 ) OR ( CHAIN G AND RESID 1:84 ) OR ( CHAIN F AND RESID 1:98 ) OR ( CHAIN I AND RESID 1:73 ) OR ( CHAIN H AND RESID 7:85 ) OR ( CHAIN K AND RESID 6:54 ) OR ( CHAIN J AND RESID 1:58 ) OR ( CHAIN M AND RESID 1:43 ) OR ( CHAIN L AND RESID 2:47 )L2 - 47
14X-RAY DIFFRACTION2( CHAIN O AND RESID 1:227 ) OR ( CHAIN N AND RESID 1:514 ) OR ( CHAIN Q AND RESID 4:147 ) OR ( CHAIN P AND RESID 4:261 ) OR ( CHAIN S AND RESID 1:98 ) OR ( CHAIN R AND RESID 5:109 ) OR ( CHAIN U AND RESID 7:85 ) OR ( CHAIN T AND RESID 1:84 ) OR ( CHAIN W AND RESID 1:58 ) OR ( CHAIN V AND RESID 1:73 ) OR ( CHAIN Y AND RESID 2:47 ) OR ( CHAIN X AND RESID 6:54 ) OR ( CHAIN Z AND RESID 1:43 )O1 - 227
15X-RAY DIFFRACTION2( CHAIN O AND RESID 1:227 ) OR ( CHAIN N AND RESID 1:514 ) OR ( CHAIN Q AND RESID 4:147 ) OR ( CHAIN P AND RESID 4:261 ) OR ( CHAIN S AND RESID 1:98 ) OR ( CHAIN R AND RESID 5:109 ) OR ( CHAIN U AND RESID 7:85 ) OR ( CHAIN T AND RESID 1:84 ) OR ( CHAIN W AND RESID 1:58 ) OR ( CHAIN V AND RESID 1:73 ) OR ( CHAIN Y AND RESID 2:47 ) OR ( CHAIN X AND RESID 6:54 ) OR ( CHAIN Z AND RESID 1:43 )N1 - 514
16X-RAY DIFFRACTION2( CHAIN O AND RESID 1:227 ) OR ( CHAIN N AND RESID 1:514 ) OR ( CHAIN Q AND RESID 4:147 ) OR ( CHAIN P AND RESID 4:261 ) OR ( CHAIN S AND RESID 1:98 ) OR ( CHAIN R AND RESID 5:109 ) OR ( CHAIN U AND RESID 7:85 ) OR ( CHAIN T AND RESID 1:84 ) OR ( CHAIN W AND RESID 1:58 ) OR ( CHAIN V AND RESID 1:73 ) OR ( CHAIN Y AND RESID 2:47 ) OR ( CHAIN X AND RESID 6:54 ) OR ( CHAIN Z AND RESID 1:43 )Q4 - 147
17X-RAY DIFFRACTION2( CHAIN O AND RESID 1:227 ) OR ( CHAIN N AND RESID 1:514 ) OR ( CHAIN Q AND RESID 4:147 ) OR ( CHAIN P AND RESID 4:261 ) OR ( CHAIN S AND RESID 1:98 ) OR ( CHAIN R AND RESID 5:109 ) OR ( CHAIN U AND RESID 7:85 ) OR ( CHAIN T AND RESID 1:84 ) OR ( CHAIN W AND RESID 1:58 ) OR ( CHAIN V AND RESID 1:73 ) OR ( CHAIN Y AND RESID 2:47 ) OR ( CHAIN X AND RESID 6:54 ) OR ( CHAIN Z AND RESID 1:43 )P4 - 261
18X-RAY DIFFRACTION2( CHAIN O AND RESID 1:227 ) OR ( CHAIN N AND RESID 1:514 ) OR ( CHAIN Q AND RESID 4:147 ) OR ( CHAIN P AND RESID 4:261 ) OR ( CHAIN S AND RESID 1:98 ) OR ( CHAIN R AND RESID 5:109 ) OR ( CHAIN U AND RESID 7:85 ) OR ( CHAIN T AND RESID 1:84 ) OR ( CHAIN W AND RESID 1:58 ) OR ( CHAIN V AND RESID 1:73 ) OR ( CHAIN Y AND RESID 2:47 ) OR ( CHAIN X AND RESID 6:54 ) OR ( CHAIN Z AND RESID 1:43 )S1 - 98
19X-RAY DIFFRACTION2( CHAIN O AND RESID 1:227 ) OR ( CHAIN N AND RESID 1:514 ) OR ( CHAIN Q AND RESID 4:147 ) OR ( CHAIN P AND RESID 4:261 ) OR ( CHAIN S AND RESID 1:98 ) OR ( CHAIN R AND RESID 5:109 ) OR ( CHAIN U AND RESID 7:85 ) OR ( CHAIN T AND RESID 1:84 ) OR ( CHAIN W AND RESID 1:58 ) OR ( CHAIN V AND RESID 1:73 ) OR ( CHAIN Y AND RESID 2:47 ) OR ( CHAIN X AND RESID 6:54 ) OR ( CHAIN Z AND RESID 1:43 )R5 - 109
20X-RAY DIFFRACTION2( CHAIN O AND RESID 1:227 ) OR ( CHAIN N AND RESID 1:514 ) OR ( CHAIN Q AND RESID 4:147 ) OR ( CHAIN P AND RESID 4:261 ) OR ( CHAIN S AND RESID 1:98 ) OR ( CHAIN R AND RESID 5:109 ) OR ( CHAIN U AND RESID 7:85 ) OR ( CHAIN T AND RESID 1:84 ) OR ( CHAIN W AND RESID 1:58 ) OR ( CHAIN V AND RESID 1:73 ) OR ( CHAIN Y AND RESID 2:47 ) OR ( CHAIN X AND RESID 6:54 ) OR ( CHAIN Z AND RESID 1:43 )U7 - 85
21X-RAY DIFFRACTION2( CHAIN O AND RESID 1:227 ) OR ( CHAIN N AND RESID 1:514 ) OR ( CHAIN Q AND RESID 4:147 ) OR ( CHAIN P AND RESID 4:261 ) OR ( CHAIN S AND RESID 1:98 ) OR ( CHAIN R AND RESID 5:109 ) OR ( CHAIN U AND RESID 7:85 ) OR ( CHAIN T AND RESID 1:84 ) OR ( CHAIN W AND RESID 1:58 ) OR ( CHAIN V AND RESID 1:73 ) OR ( CHAIN Y AND RESID 2:47 ) OR ( CHAIN X AND RESID 6:54 ) OR ( CHAIN Z AND RESID 1:43 )T1 - 84
22X-RAY DIFFRACTION2( CHAIN O AND RESID 1:227 ) OR ( CHAIN N AND RESID 1:514 ) OR ( CHAIN Q AND RESID 4:147 ) OR ( CHAIN P AND RESID 4:261 ) OR ( CHAIN S AND RESID 1:98 ) OR ( CHAIN R AND RESID 5:109 ) OR ( CHAIN U AND RESID 7:85 ) OR ( CHAIN T AND RESID 1:84 ) OR ( CHAIN W AND RESID 1:58 ) OR ( CHAIN V AND RESID 1:73 ) OR ( CHAIN Y AND RESID 2:47 ) OR ( CHAIN X AND RESID 6:54 ) OR ( CHAIN Z AND RESID 1:43 )W1 - 58
23X-RAY DIFFRACTION2( CHAIN O AND RESID 1:227 ) OR ( CHAIN N AND RESID 1:514 ) OR ( CHAIN Q AND RESID 4:147 ) OR ( CHAIN P AND RESID 4:261 ) OR ( CHAIN S AND RESID 1:98 ) OR ( CHAIN R AND RESID 5:109 ) OR ( CHAIN U AND RESID 7:85 ) OR ( CHAIN T AND RESID 1:84 ) OR ( CHAIN W AND RESID 1:58 ) OR ( CHAIN V AND RESID 1:73 ) OR ( CHAIN Y AND RESID 2:47 ) OR ( CHAIN X AND RESID 6:54 ) OR ( CHAIN Z AND RESID 1:43 )V1 - 73
24X-RAY DIFFRACTION2( CHAIN O AND RESID 1:227 ) OR ( CHAIN N AND RESID 1:514 ) OR ( CHAIN Q AND RESID 4:147 ) OR ( CHAIN P AND RESID 4:261 ) OR ( CHAIN S AND RESID 1:98 ) OR ( CHAIN R AND RESID 5:109 ) OR ( CHAIN U AND RESID 7:85 ) OR ( CHAIN T AND RESID 1:84 ) OR ( CHAIN W AND RESID 1:58 ) OR ( CHAIN V AND RESID 1:73 ) OR ( CHAIN Y AND RESID 2:47 ) OR ( CHAIN X AND RESID 6:54 ) OR ( CHAIN Z AND RESID 1:43 )Y2 - 47
25X-RAY DIFFRACTION2( CHAIN O AND RESID 1:227 ) OR ( CHAIN N AND RESID 1:514 ) OR ( CHAIN Q AND RESID 4:147 ) OR ( CHAIN P AND RESID 4:261 ) OR ( CHAIN S AND RESID 1:98 ) OR ( CHAIN R AND RESID 5:109 ) OR ( CHAIN U AND RESID 7:85 ) OR ( CHAIN T AND RESID 1:84 ) OR ( CHAIN W AND RESID 1:58 ) OR ( CHAIN V AND RESID 1:73 ) OR ( CHAIN Y AND RESID 2:47 ) OR ( CHAIN X AND RESID 6:54 ) OR ( CHAIN Z AND RESID 1:43 )X6 - 54
26X-RAY DIFFRACTION2( CHAIN O AND RESID 1:227 ) OR ( CHAIN N AND RESID 1:514 ) OR ( CHAIN Q AND RESID 4:147 ) OR ( CHAIN P AND RESID 4:261 ) OR ( CHAIN S AND RESID 1:98 ) OR ( CHAIN R AND RESID 5:109 ) OR ( CHAIN U AND RESID 7:85 ) OR ( CHAIN T AND RESID 1:84 ) OR ( CHAIN W AND RESID 1:58 ) OR ( CHAIN V AND RESID 1:73 ) OR ( CHAIN Y AND RESID 2:47 ) OR ( CHAIN X AND RESID 6:54 ) OR ( CHAIN Z AND RESID 1:43 )Z1 - 43

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万見について

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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