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- PDB-5cod: Bovine heart complex I membrane domain -

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Basic information

Entry
Database: PDB / ID: 5cod
TitleBovine heart complex I membrane domain
Components
  • (NADH-ubiquinone oxidoreductase chain ...) x 2
  • (Unknown structure) x 11
  • SDAP
KeywordsOXIDOREDUCTASE / Animals / Cattle / Electron Transport Complex I / Mitochondria / Heart / Models / Molecular / Protein Structure / Tertiary / Protein Subunits
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.74 Å
AuthorsZhu, J. / Hirst, J. / King, M.S. / Yu, M. / Leslie, A.G.W. / Klipcan, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structure of subcomplex I beta of mammalian respiratory complex I leads to new supernumerary subunit assignments.
Authors: Zhu, J. / King, M.S. / Yu, M. / Klipcan, L. / Leslie, A.G. / Hirst, J.
History
DepositionJul 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details
Revision 2.0Jul 8, 2026Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Non-polymer description / Polymer sequence / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_name_com / entity_poly / entity_poly_seq / exptl_crystal / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conf / struct_conn / struct_mon_prot_cis / struct_ncs_dom_lim / struct_ref_seq / struct_sheet_range
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 / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_unobs_or_zero_occ_residues.auth_comp_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.label_comp_id / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_peptide_omega.auth_comp_id_1 / _pdbx_validate_peptide_omega.auth_comp_id_2 / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_mon_prot_cis.auth_comp_id / _struct_mon_prot_cis.label_comp_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_auth_comp_id_2 / _struct_mon_prot_cis.pdbx_label_comp_id_2 / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ncs_dom_lim.beg_auth_comp_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_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L1: NADH-ubiquinone oxidoreductase chain 5
M1: NADH-ubiquinone oxidoreductase chain 4
f1: Unknown structure
g1: Unknown structure
h1: Unknown structure
i1: Unknown structure
j1: Unknown structure
k1: Unknown structure
l1: Unknown structure
U1: SDAP
n1: Unknown structure
o1: Unknown structure
p1: Unknown structure
s1: Unknown structure
t1: Unknown structure
u1: Unknown structure
v1: Unknown structure
w1: Unknown structure
BA: Unknown structure
L2: NADH-ubiquinone oxidoreductase chain 5
M2: NADH-ubiquinone oxidoreductase chain 4
f2: Unknown structure
g2: Unknown structure
h2: Unknown structure
i2: Unknown structure
j2: Unknown structure
k2: Unknown structure
l2: Unknown structure
U2: SDAP
n2: Unknown structure
o2: Unknown structure
p2: Unknown structure
s2: Unknown structure
t2: Unknown structure
u2: Unknown structure
v2: Unknown structure
w2: Unknown structure
BB: Unknown structure
L3: NADH-ubiquinone oxidoreductase chain 5
M3: NADH-ubiquinone oxidoreductase chain 4
f3: Unknown structure
g3: Unknown structure
h3: Unknown structure
i3: Unknown structure
j3: Unknown structure
k3: Unknown structure
l3: Unknown structure
U3: SDAP
n3: Unknown structure
o3: Unknown structure
p3: Unknown structure
s3: Unknown structure
t3: Unknown structure
u3: Unknown structure
v3: Unknown structure
w3: Unknown structure
BC: Unknown structure
L4: NADH-ubiquinone oxidoreductase chain 5
M4: NADH-ubiquinone oxidoreductase chain 4
f4: Unknown structure
g4: Unknown structure
h4: Unknown structure
i4: Unknown structure
j4: Unknown structure
k4: Unknown structure
l4: Unknown structure
U4: SDAP
n4: Unknown structure
o4: Unknown structure
p4: Unknown structure
s4: Unknown structure
t4: Unknown structure
u4: Unknown structure
v4: Unknown structure
w4: Unknown structure
BD: Unknown structure
L5: NADH-ubiquinone oxidoreductase chain 5
M5: NADH-ubiquinone oxidoreductase chain 4
f5: Unknown structure
g5: Unknown structure
h5: Unknown structure
i5: Unknown structure
j5: Unknown structure
k5: Unknown structure
l5: Unknown structure
U5: SDAP
n5: Unknown structure
o5: Unknown structure
p5: Unknown structure
s5: Unknown structure
t5: Unknown structure
u5: Unknown structure
v5: Unknown structure
w5: Unknown structure
BE: Unknown structure
L6: NADH-ubiquinone oxidoreductase chain 5
M6: NADH-ubiquinone oxidoreductase chain 4
f6: Unknown structure
g6: Unknown structure
h6: Unknown structure
i6: Unknown structure
j6: Unknown structure
k6: Unknown structure
l6: Unknown structure
U6: SDAP
n6: Unknown structure
o6: Unknown structure
p6: Unknown structure
s6: Unknown structure
t6: Unknown structure
u6: Unknown structure
v6: Unknown structure
w6: Unknown structure
BF: Unknown structure


Theoretical massNumber of molelcules
Total (without water)1,070,376114
Polymers1,070,376114
Non-polymers00
Water00
1
L1: NADH-ubiquinone oxidoreductase chain 5
M1: NADH-ubiquinone oxidoreductase chain 4
f1: Unknown structure
g1: Unknown structure
h1: Unknown structure
i1: Unknown structure
j1: Unknown structure
k1: Unknown structure
l1: Unknown structure
U1: SDAP
n1: Unknown structure
o1: Unknown structure
p1: Unknown structure
s1: Unknown structure
t1: Unknown structure
u1: Unknown structure
v1: Unknown structure
w1: Unknown structure
BA: Unknown structure


Theoretical massNumber of molelcules
Total (without water)178,39619
Polymers178,39619
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
L2: NADH-ubiquinone oxidoreductase chain 5
M2: NADH-ubiquinone oxidoreductase chain 4
f2: Unknown structure
g2: Unknown structure
h2: Unknown structure
i2: Unknown structure
j2: Unknown structure
k2: Unknown structure
l2: Unknown structure
U2: SDAP
n2: Unknown structure
o2: Unknown structure
p2: Unknown structure
s2: Unknown structure
t2: Unknown structure
u2: Unknown structure
v2: Unknown structure
w2: Unknown structure
BB: Unknown structure


Theoretical massNumber of molelcules
Total (without water)178,39619
Polymers178,39619
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
L3: NADH-ubiquinone oxidoreductase chain 5
M3: NADH-ubiquinone oxidoreductase chain 4
f3: Unknown structure
g3: Unknown structure
h3: Unknown structure
i3: Unknown structure
j3: Unknown structure
k3: Unknown structure
l3: Unknown structure
U3: SDAP
n3: Unknown structure
o3: Unknown structure
p3: Unknown structure
s3: Unknown structure
t3: Unknown structure
u3: Unknown structure
v3: Unknown structure
w3: Unknown structure
BC: Unknown structure


Theoretical massNumber of molelcules
Total (without water)178,39619
Polymers178,39619
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
L4: NADH-ubiquinone oxidoreductase chain 5
M4: NADH-ubiquinone oxidoreductase chain 4
f4: Unknown structure
g4: Unknown structure
h4: Unknown structure
i4: Unknown structure
j4: Unknown structure
k4: Unknown structure
l4: Unknown structure
U4: SDAP
n4: Unknown structure
o4: Unknown structure
p4: Unknown structure
s4: Unknown structure
t4: Unknown structure
u4: Unknown structure
v4: Unknown structure
w4: Unknown structure
BD: Unknown structure


Theoretical massNumber of molelcules
Total (without water)178,39619
Polymers178,39619
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
L5: NADH-ubiquinone oxidoreductase chain 5
M5: NADH-ubiquinone oxidoreductase chain 4
f5: Unknown structure
g5: Unknown structure
h5: Unknown structure
i5: Unknown structure
j5: Unknown structure
k5: Unknown structure
l5: Unknown structure
U5: SDAP
n5: Unknown structure
o5: Unknown structure
p5: Unknown structure
s5: Unknown structure
t5: Unknown structure
u5: Unknown structure
v5: Unknown structure
w5: Unknown structure
BE: Unknown structure


Theoretical massNumber of molelcules
Total (without water)178,39619
Polymers178,39619
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
L6: NADH-ubiquinone oxidoreductase chain 5
M6: NADH-ubiquinone oxidoreductase chain 4
f6: Unknown structure
g6: Unknown structure
h6: Unknown structure
i6: Unknown structure
j6: Unknown structure
k6: Unknown structure
l6: Unknown structure
U6: SDAP
n6: Unknown structure
o6: Unknown structure
p6: Unknown structure
s6: Unknown structure
t6: Unknown structure
u6: Unknown structure
v6: Unknown structure
w6: Unknown structure
BF: Unknown structure


Theoretical massNumber of molelcules
Total (without water)178,39619
Polymers178,39619
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)244.832, 251.414, 412.034
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
12
22
32
42
52
62
72
82
92
102
112
122
13
23
33
43
53
63
14
24
34
44
54
64
74
84
94
104
114
124
134
144
154
164
174
184
194
204
214
224
234
244
254
264
274
284
294
304
314
324
334
344
354
364
374
384
394
404
414
424
434
444
454
464
474
484
494
504
514
524
534
544
15
25
35
45
55
65
75
85
95
105
115
125
16
26
36
46
56
66
76
86
96
106
116
126
17
27
37
47
57
67
77
87
97
107
117
127

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111UNKUNKUNKUNKchain 'BA'BAS528 - 5461 - 19
121UNKUNKUNKUNKchain 'BA'BAS548 - 56221 - 35
131UNKUNKUNKUNKchain 'BA'BAS571 - 58637 - 52
141UNKUNKUNKUNKchain 'BA'BAS1588 - 162554 - 91
151UNKUNKUNKUNKchain 'BA'BAS1632 - 163893 - 99
161UNKUNKUNKUNKchain 'BA'BAS1642 - 1648101 - 107
171UNKUNKUNKUNKchain 'BA'BAS1651 - 1658109 - 116
181UNKUNKUNKUNKchain 'BA'BAS1660 - 1667118 - 125
191UNKUNKUNKUNKchain 'BA'BAS1669 - 1687127 - 145
2101UNKUNKUNKUNKchain 'BB'BBLA528 - 5461 - 19
2111UNKUNKUNKUNKchain 'BB'BBLA548 - 56221 - 35
2121UNKUNKUNKUNKchain 'BB'BBLA571 - 58637 - 52
2131UNKUNKUNKUNKchain 'BB'BBLA1588 - 162554 - 91
2141UNKUNKUNKUNKchain 'BB'BBLA1632 - 163893 - 99
2151UNKUNKUNKUNKchain 'BB'BBLA1642 - 1648101 - 107
2161UNKUNKUNKUNKchain 'BB'BBLA1651 - 1658109 - 116
2171UNKUNKUNKUNKchain 'BB'BBLA1660 - 1667118 - 125
2181UNKUNKUNKUNKchain 'BB'BBLA1669 - 1687127 - 145
3191UNKUNKUNKUNKchain 'BC'BCEB528 - 5461 - 19
3201UNKUNKUNKUNKchain 'BC'BCEB548 - 56221 - 35
3211UNKUNKUNKUNKchain 'BC'BCEB571 - 58637 - 52
3221UNKUNKUNKUNKchain 'BC'BCEB1588 - 162554 - 91
3231UNKUNKUNKUNKchain 'BC'BCEB1632 - 163893 - 99
3241UNKUNKUNKUNKchain 'BC'BCEB1642 - 1648101 - 107
3251UNKUNKUNKUNKchain 'BC'BCEB1651 - 1658109 - 116
3261UNKUNKUNKUNKchain 'BC'BCEB1660 - 1667118 - 125
3271UNKUNKUNKUNKchain 'BC'BCEB1669 - 1687127 - 145
4281UNKUNKUNKUNKchain 'BD'BDXB528 - 5461 - 19
4291UNKUNKUNKUNKchain 'BD'BDXB548 - 56221 - 35
4301UNKUNKUNKUNKchain 'BD'BDXB571 - 58637 - 52
4311UNKUNKUNKUNKchain 'BD'BDXB1588 - 162554 - 91
4321UNKUNKUNKUNKchain 'BD'BDXB1632 - 163893 - 99
4331UNKUNKUNKUNKchain 'BD'BDXB1642 - 1648101 - 107
4341UNKUNKUNKUNKchain 'BD'BDXB1651 - 1658109 - 116
4351UNKUNKUNKUNKchain 'BD'BDXB1660 - 1667118 - 125
4361UNKUNKUNKUNKchain 'BD'BDXB1669 - 1687127 - 145
5371UNKUNKUNKUNKchain 'BE'BEQC528 - 5461 - 19
5381UNKUNKUNKUNKchain 'BE'BEQC548 - 56221 - 35
5391UNKUNKUNKUNKchain 'BE'BEQC571 - 58637 - 52
5401UNKUNKUNKUNKchain 'BE'BEQC1588 - 162554 - 91
5411UNKUNKUNKUNKchain 'BE'BEQC1632 - 163893 - 99
5421UNKUNKUNKUNKchain 'BE'BEQC1642 - 1648101 - 107
5431UNKUNKUNKUNKchain 'BE'BEQC1651 - 1658109 - 116
5441UNKUNKUNKUNKchain 'BE'BEQC1660 - 1667118 - 125
5451UNKUNKUNKUNKchain 'BE'BEQC1669 - 1687127 - 145
6461UNKUNKUNKUNKchain 'BF'BFJD528 - 5461 - 19
6471UNKUNKUNKUNKchain 'BF'BFJD548 - 56221 - 35
6481UNKUNKUNKUNKchain 'BF'BFJD571 - 58637 - 52
6491UNKUNKUNKUNKchain 'BF'BFJD1588 - 162554 - 91
6501UNKUNKUNKUNKchain 'BF'BFJD1632 - 163893 - 99
6511UNKUNKUNKUNKchain 'BF'BFJD1642 - 1648101 - 107
6521UNKUNKUNKUNKchain 'BF'BFJD1651 - 1658109 - 116
6531UNKUNKUNKUNKchain 'BF'BFJD1660 - 1667118 - 125
6541UNKUNKUNKUNKchain 'BF'BFJD1669 - 1687127 - 145
1552ASNASNPROPROchain 'L1'L1A5 - 212 - 18
1562METMETASNASNchain 'L1'L1A28 - 21320 - 205
1572SERSERHISHISchain 'L1'L1A216 - 357207 - 348
1582LEULEULEULEUchain 'L1'L1A363 - 399350 - 386
1592SERSERILEILEchain 'L1'L1A489 - 512469 - 492
2602ASNASNPROPROchain 'L2'L2T5 - 212 - 18
2612METMETASNASNchain 'L2'L2T28 - 21320 - 205
2622SERSERHISHISchain 'L2'L2T216 - 357207 - 348
2632LEULEULEULEUchain 'L2'L2T363 - 399350 - 386
2642SERSERILEILEchain 'L2'L2T489 - 512469 - 492
3652ASNASNPROPROchain 'L3'L3MA5 - 212 - 18
3662METMETASNASNchain 'L3'L3MA28 - 21320 - 205
3672SERSERHISHISchain 'L3'L3MA216 - 357207 - 348
3682LEULEULEULEUchain 'L3'L3MA363 - 399350 - 386
3692SERSERILEILEchain 'L3'L3MA489 - 512469 - 492
4702ASNASNPROPROchain 'L4'L4FB5 - 212 - 18
4712METMETASNASNchain 'L4'L4FB28 - 21320 - 205
4722SERSERHISHISchain 'L4'L4FB216 - 357207 - 348
4732LEULEULEULEUchain 'L4'L4FB363 - 399350 - 386
4742SERSERILEILEchain 'L4'L4FB489 - 512469 - 492
5752ASNASNPROPROchain 'L5'L5YB5 - 212 - 18
5762METMETASNASNchain 'L5'L5YB28 - 21320 - 205
5772SERSERHISHISchain 'L5'L5YB216 - 357207 - 348
5782LEULEULEULEUchain 'L5'L5YB363 - 399350 - 386
5792SERSERILEILEchain 'L5'L5YB489 - 512469 - 492
6802ASNASNPROPROchain 'L6'L6RC5 - 212 - 18
6812METMETASNASNchain 'L6'L6RC28 - 21320 - 205
6822SERSERHISHISchain 'L6'L6RC216 - 357207 - 348
6832LEULEULEULEUchain 'L6'L6RC363 - 399350 - 386
6842SERSERILEILEchain 'L6'L6RC489 - 512469 - 492
7852ASNASNPHEPHEchain 'M1'M1B20 - 3620 - 36
7862ASNASNSERSERchain 'M1'M1B43 - 22843 - 228
7872LEULEUTHRTHRchain 'M1'M1B231 - 372231 - 372
7882GLUGLUTHRTHRchain 'M1'M1B378 - 414378 - 414
7892UNKUNKILEILEchain 'M1'M1B431 - 454431 - 454
8902ASNASNPHEPHEchain 'M2'M2U20 - 3620 - 36
8912ASNASNSERSERchain 'M2'M2U43 - 22843 - 228
8922LEULEUTHRTHRchain 'M2'M2U231 - 372231 - 372
8932GLUGLUTHRTHRchain 'M2'M2U378 - 414378 - 414
8942UNKUNKILEILEchain 'M2'M2U431 - 454431 - 454
9952ASNASNPHEPHEchain 'M3'M3NA20 - 3620 - 36
9962ASNASNSERSERchain 'M3'M3NA43 - 22843 - 228
9972LEULEUTHRTHRchain 'M3'M3NA231 - 372231 - 372
9982GLUGLUTHRTHRchain 'M3'M3NA378 - 414378 - 414
9992UNKUNKILEILEchain 'M3'M3NA431 - 454431 - 454
101002ASNASNPHEPHEchain 'M4'M4GB20 - 3620 - 36
101012ASNASNSERSERchain 'M4'M4GB43 - 22843 - 228
101022LEULEUTHRTHRchain 'M4'M4GB231 - 372231 - 372
101032GLUGLUTHRTHRchain 'M4'M4GB378 - 414378 - 414
101042UNKUNKILEILEchain 'M4'M4GB431 - 454431 - 454
111052ASNASNPHEPHEchain 'M5'M5ZB20 - 3620 - 36
111062ASNASNSERSERchain 'M5'M5ZB43 - 22843 - 228
111072LEULEUTHRTHRchain 'M5'M5ZB231 - 372231 - 372
111082GLUGLUTHRTHRchain 'M5'M5ZB378 - 414378 - 414
111092UNKUNKILEILEchain 'M5'M5ZB431 - 454431 - 454
121102ASNASNPHEPHEchain 'M6'M6SC20 - 3620 - 36
121112ASNASNSERSERchain 'M6'M6SC43 - 22843 - 228
121122LEULEUTHRTHRchain 'M6'M6SC231 - 372231 - 372
121132GLUGLUTHRTHRchain 'M6'M6SC378 - 414378 - 414
121142UNKUNKILEILEchain 'M6'M6SC431 - 454431 - 454
11153UNKUNKUNKUNKchain 'U1'U1J8 - 811 - 74
21163UNKUNKUNKUNKchain 'U2'U2CA8 - 811 - 74
31173UNKUNKUNKUNKchain 'U3'U3VA8 - 811 - 74
41183UNKUNKUNKUNKchain 'U4'U4OB8 - 811 - 74
51193UNKUNKUNKUNKchain 'U5'U5HC8 - 811 - 74
61203UNKUNKUNKUNKchain 'U6'U6AD8 - 811 - 74
11214UNKUNKUNKUNKchain 'f1'f1C5 - 295 - 29
21224UNKUNKUNKUNKchain 'f2'f2V5 - 295 - 29
31234UNKUNKUNKUNKchain 'f3'f3OA5 - 295 - 29
41244UNKUNKUNKUNKchain 'f4'f4HB5 - 295 - 29
51254UNKUNKUNKUNKchain 'f5'f5AC5 - 295 - 29
61264UNKUNKUNKUNKchain 'f6'f6TC5 - 295 - 29
71274UNKUNKUNKUNKchain 'h1'h1E5 - 295 - 29
81284UNKUNKUNKUNKchain 'h2'h2X5 - 295 - 29
91294UNKUNKUNKUNKchain 'h3'h3QA5 - 295 - 29
101304UNKUNKUNKUNKchain 'h4'h4JB5 - 295 - 29
111314UNKUNKUNKUNKchain 'h5'h5CC5 - 295 - 29
121324UNKUNKUNKUNKchain 'h6'h6VC5 - 295 - 29
131334UNKUNKUNKUNKchain 'i1'i1F5 - 295 - 29
141344UNKUNKUNKUNKchain 'i2'i2Y5 - 295 - 29
151354UNKUNKUNKUNKchain 'i3'i3RA5 - 295 - 29
161364UNKUNKUNKUNKchain 'i4'i4KB5 - 295 - 29
171374UNKUNKUNKUNKchain 'i5'i5DC5 - 295 - 29
181384UNKUNKUNKUNKchain 'i6'i6WC5 - 295 - 29
191394UNKUNKUNKUNKchain 'j1'j1G3 - 273 - 27
201404UNKUNKUNKUNKchain 'j2'j2Z3 - 273 - 27
211414UNKUNKUNKUNKchain 'j3'j3SA3 - 273 - 27
221424UNKUNKUNKUNKchain 'j4'j4LB3 - 273 - 27
231434UNKUNKUNKUNKchain 'j5'j5EC3 - 273 - 27
241444UNKUNKUNKUNKchain 'j6'j6XC3 - 273 - 27
251454UNKUNKUNKUNKchain 'k1'k1H3 - 273 - 27
261464UNKUNKUNKUNKchain 'k2'k2AA3 - 273 - 27
271474UNKUNKUNKUNKchain 'k3'k3TA3 - 273 - 27
281484UNKUNKUNKUNKchain 'k4'k4MB3 - 273 - 27
291494UNKUNKUNKUNKchain 'k5'k5FC3 - 273 - 27
301504UNKUNKUNKUNKchain 'k6'k6YC3 - 273 - 27
311514UNKUNKUNKUNKchain 'p1'p1M3 - 273 - 27
321524UNKUNKUNKUNKchain 'p2'p2FA3 - 273 - 27
331534UNKUNKUNKUNKchain 'p3'p3YA3 - 273 - 27
341544UNKUNKUNKUNKchain 'p4'p4RB3 - 273 - 27
351554UNKUNKUNKUNKchain 'p5'p5KC3 - 273 - 27
361564UNKUNKUNKUNKchain 'p6'p6DD3 - 273 - 27
371574UNKUNKUNKUNKchain 's1's1N3 - 273 - 27
381584UNKUNKUNKUNKchain 's2's2GA3 - 273 - 27
391594UNKUNKUNKUNKchain 's3's3ZA3 - 273 - 27
401604UNKUNKUNKUNKchain 's4's4SB3 - 273 - 27
411614UNKUNKUNKUNKchain 's5's5LC3 - 273 - 27
421624UNKUNKUNKUNKchain 's6's6ED3 - 273 - 27
431634UNKUNKUNKUNKchain 'v1'v1Q7 - 317 - 31
441644UNKUNKUNKUNKchain 'v2'v2JA7 - 317 - 31
451654UNKUNKUNKUNKchain 'v3'v3CB7 - 317 - 31
461664UNKUNKUNKUNKchain 'v4'v4VB7 - 317 - 31
471674UNKUNKUNKUNKchain 'v5'v5OC7 - 317 - 31
481684UNKUNKUNKUNKchain 'v6'v6HD7 - 317 - 31
491694UNKUNKUNKUNKchain 'w1'w1R2 - 262 - 26
501704UNKUNKUNKUNKchain 'w2'w2KA2 - 262 - 26
511714UNKUNKUNKUNKchain 'w3'w3DB2 - 262 - 26
521724UNKUNKUNKUNKchain 'w4'w4WB2 - 262 - 26
531734UNKUNKUNKUNKchain 'w5'w5PC2 - 262 - 26
541744UNKUNKUNKUNKchain 'w6'w6ID2 - 262 - 26
11755UNKUNKUNKUNKchain 'g1'g1D3 - 213 - 21
21765UNKUNKUNKUNKchain 'g2'g2W3 - 213 - 21
31775UNKUNKUNKUNKchain 'g3'g3PA3 - 213 - 21
41785UNKUNKUNKUNKchain 'g4'g4IB3 - 213 - 21
51795UNKUNKUNKUNKchain 'g5'g5BC3 - 213 - 21
61805UNKUNKUNKUNKchain 'g6'g6UC3 - 213 - 21
71815UNKUNKUNKUNKchain 'o1'o1L2 - 202 - 20
81825UNKUNKUNKUNKchain 'o2'o2EA2 - 202 - 20
91835UNKUNKUNKUNKchain 'o3'o3XA2 - 202 - 20
101845UNKUNKUNKUNKchain 'o4'o4QB2 - 202 - 20
111855UNKUNKUNKUNKchain 'o5'o5JC2 - 202 - 20
121865UNKUNKUNKUNKchain 'o6'o6CD2 - 202 - 20
11876UNKUNKUNKUNKchain 'l1'l1I12 - 231 - 12
21886UNKUNKUNKUNKchain 'l2'l2BA12 - 231 - 12
31896UNKUNKUNKUNKchain 'l3'l3UA12 - 231 - 12
41906UNKUNKUNKUNKchain 'l4'l4NB12 - 231 - 12
51916UNKUNKUNKUNKchain 'l5'l5GC12 - 231 - 12
61926UNKUNKUNKUNKchain 'l6'l6ZC12 - 231 - 12
71936UNKUNKUNKUNKchain 'u1'u1P3 - 143 - 14
81946UNKUNKUNKUNKchain 'u2'u2IA3 - 143 - 14
91956UNKUNKUNKUNKchain 'u3'u3BB3 - 143 - 14
101966UNKUNKUNKUNKchain 'u4'u4UB3 - 143 - 14
111976UNKUNKUNKUNKchain 'u5'u5NC3 - 143 - 14
121986UNKUNKUNKUNKchain 'u6'u6GD3 - 143 - 14
11997UNKUNKUNKUNKchain 'n1'n1K4 - 584 - 58
22007UNKUNKUNKUNKchain 'n2'n2DA4 - 584 - 58
32017UNKUNKUNKUNKchain 'n3'n3WA4 - 584 - 58
42027UNKUNKUNKUNKchain 'n4'n4PB4 - 584 - 58
52037UNKUNKUNKUNKchain 'n5'n5IC4 - 584 - 58
62047UNKUNKUNKUNKchain 'n6'n6BD4 - 584 - 58
72057UNKUNKUNKUNKchain 't1't1O2 - 562 - 56
82067UNKUNKUNKUNKchain 't2't2HA2 - 562 - 56
92077UNKUNKUNKUNKchain 't3't3AB2 - 562 - 56
102087UNKUNKUNKUNKchain 't4't4TB2 - 562 - 56
112097UNKUNKUNKUNKchain 't5't5MC2 - 562 - 56
122107UNKUNKUNKUNKchain 't6't6FD2 - 562 - 56

NCS ensembles :
ID
1
2
3
4
5
6
7

-
Components

-
NADH-ubiquinone oxidoreductase chain ... , 2 types, 12 molecules L1L2L3L4L5L6M1M2M3M4M5M6

#1: Protein
NADH-ubiquinone oxidoreductase chain 5


Mass: 68290.844 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
#2: Protein
NADH-ubiquinone oxidoreductase chain 4


Mass: 51757.453 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)

-
Protein/peptide , 8 types, 78 molecules f1h1i1f2h2i2f3h3i3f4h4i4f5h5i5f6h6i6g1g2g3g4g5g6j1k1p1s1j2k2...

#3: Protein/peptide
Unknown structure


Mass: 2571.161 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
#4: Protein/peptide
Unknown structure


Mass: 1890.321 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
#5: Protein/peptide ...
Unknown structure


Mass: 2400.951 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
#6: Protein/peptide
Unknown structure


Mass: 1124.378 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
#9: Protein/peptide
Unknown structure


Mass: 1805.216 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
#11: Protein/peptide
Unknown structure


Mass: 1294.587 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
#12: Protein/peptide
Unknown structure


Mass: 2741.370 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
#13: Protein/peptide
Unknown structure


Mass: 2315.846 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)

-
Protein , 4 types, 24 molecules U1U2U3U4U5U6n1n2n3n4n5n6t1t2t3t4t5t6BABBBCBDBEBF

#7: Protein
SDAP


Mass: 7507.245 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
#8: Protein
Unknown structure


Mass: 5039.203 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
#10: Protein
Unknown structure


Mass: 4868.993 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
#14: Protein
Unknown structure


Mass: 12443.330 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)

-
Details

Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 5.92 Å3/Da / Density % sol: 79.24 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: Tris-HCl, magnesium chloride, sodium chloride, PEG 3350, n-Dodecyl beta-D-maltoside

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 6.74→49.4 Å / Num. obs: 44280 / % possible obs: 97.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 495.710145503 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.4
Reflection shellResolution: 6.8→7.2 Å / Rmerge(I) obs: 1.27

-
Processing

Software
NameVersionClassification
XDSdata reduction
MOSFLMdata reduction
PHENIX1.9_1692refinement
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4uq8

4uq8


Resolution: 6.74→41.6873198321 Å / SU ML: 1.73175135834 / Cross valid method: FREE R-VALUE / σ(F): 1.3388412943 / Phase error: 49.9623021003
RfactorNum. reflection% reflection
Rfree0.434647338379 2222 5.03409683047 %
Rwork0.424796773066 41917 -
obs0.425205947788 44139 97.1582654634 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 100 Å2
Refinement stepCycle: LAST / Resolution: 6.74→41.6873198321 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms48030 0 0 0 48030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011729072265947838
X-RAY DIFFRACTIONf_angle_d2.1766345570466666
X-RAY DIFFRACTIONf_chiral_restr0.1124141969959606
X-RAY DIFFRACTIONf_plane_restr0.009454059401339414
X-RAY DIFFRACTIONf_dihedral_angle_d5.879876933959414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6.7387-6.88460.4765913053211300.4541908537492320X-RAY DIFFRACTION87.3751783167
6.8846-7.0440.4409014674231400.4529147302782625X-RAY DIFFRACTION99.353215954
7.044-7.21930.478487780711380.4408705188312663X-RAY DIFFRACTION99.0102509721
7.2193-7.41340.4328250305631380.4429524024622632X-RAY DIFFRACTION99.0701001431
7.4134-7.63030.4705688845181430.4541199650822654X-RAY DIFFRACTION98.8688582538
7.6303-7.8750.4363499093791370.4667652353032615X-RAY DIFFRACTION98.9928057554
7.875-8.15450.407108040751370.4341636001822634X-RAY DIFFRACTION98.506932101
8.1545-8.47830.4133200537541310.4049025767992640X-RAY DIFFRACTION98.4019886364
8.4783-8.86070.3795458041841450.3937692019032630X-RAY DIFFRACTION98.6140724947
8.8607-9.32290.4007843984241420.3870703478162663X-RAY DIFFRACTION98.872047938
9.3229-9.89970.3565942829061440.3539872336762642X-RAY DIFFRACTION98.7593052109
9.8997-10.65230.3251682934631370.3416300606392695X-RAY DIFFRACTION98.7447698745
10.6523-11.70270.4176303307561440.3609966786282645X-RAY DIFFRACTION97.7910238429
11.7027-13.34720.4193036965431400.3959811405612651X-RAY DIFFRACTION97.1796657382
13.3472-16.63630.4897821761141450.4501080645972718X-RAY DIFFRACTION98.4525447043
16.6363-41.68810.5264388870461310.523674890132490X-RAY DIFFRACTION87.1632856668

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