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- PDB-7m5c: Crystal Structure of human BAK in complex with WT BAK BH3 peptide -

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Basic information

Entry
Database: PDB / ID: 7m5c
TitleCrystal Structure of human BAK in complex with WT BAK BH3 peptide
Components(Bcl-2 homologous antagonist/killer) x 2
KeywordsAPOPTOSIS / protein-peptide complex
Function / homology
Function and homology information


Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / limb morphogenesis / Release of apoptotic factors from the mitochondria ...Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / limb morphogenesis / Release of apoptotic factors from the mitochondria / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / establishment or maintenance of transmembrane electrochemical gradient / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / B cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / activation of cysteine-type endopeptidase activity / endoplasmic reticulum calcium ion homeostasis / positive regulation of endoplasmic reticulum unfolded protein response / regulation of mitochondrial membrane permeability / calcium ion transport into cytosol / response to UV-C / mitochondrial fusion / fibroblast apoptotic process / Bcl-2 family protein complex / myeloid cell homeostasis / positive regulation of calcium ion transport into cytosol / porin activity / thymocyte apoptotic process / pore complex / negative regulation of release of cytochrome c from mitochondria / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / positive regulation of proteolysis / vagina development / B cell homeostasis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to unfolded protein / blood vessel remodeling / animal organ regeneration / Pyroptosis / negative regulation of peptidyl-serine phosphorylation / extrinsic apoptotic signaling pathway in absence of ligand / heat shock protein binding / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / epithelial cell proliferation / establishment of localization in cell / apoptotic signaling pathway / response to gamma radiation / positive regulation of protein-containing complex assembly / response to hydrogen peroxide / response to organic cyclic compound / cellular response to mechanical stimulus / cellular response to UV / intrinsic apoptotic signaling pathway in response to DNA damage / protein-folding chaperone binding / response to ethanol / mitochondrial outer membrane / transmembrane transporter binding / regulation of cell cycle / response to xenobiotic stimulus / positive regulation of apoptotic process / protein heterodimerization activity / negative regulation of cell population proliferation / negative regulation of gene expression / apoptotic process / protein-containing complex binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like ...Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
Similarity search - Domain/homology
COPPER (II) ION / Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsSingh, G. / Aggarwal, A. / Moldoveanu, T.
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis of BAK activation in mitochondrial apoptosis initiation.
Authors: Singh, G. / Guibao, C.D. / Seetharaman, J. / Aggarwal, A. / Grace, C.R. / McNamara, D.E. / Vaithiyalingam, S. / Waddell, M.B. / Moldoveanu, T.
History
DepositionMar 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bcl-2 homologous antagonist/killer
B: Bcl-2 homologous antagonist/killer
C: Bcl-2 homologous antagonist/killer
D: Bcl-2 homologous antagonist/killer
E: Bcl-2 homologous antagonist/killer
F: Bcl-2 homologous antagonist/killer
G: Bcl-2 homologous antagonist/killer
H: Bcl-2 homologous antagonist/killer
I: Bcl-2 homologous antagonist/killer
J: Bcl-2 homologous antagonist/killer
K: Bcl-2 homologous antagonist/killer
L: Bcl-2 homologous antagonist/killer
M: Bcl-2 homologous antagonist/killer
N: Bcl-2 homologous antagonist/killer
O: Bcl-2 homologous antagonist/killer
P: Bcl-2 homologous antagonist/killer
Q: Bcl-2 homologous antagonist/killer
R: Bcl-2 homologous antagonist/killer
S: Bcl-2 homologous antagonist/killer
T: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,04037
Polymers213,69920
Non-polymers1,34017
Water0
1
A: Bcl-2 homologous antagonist/killer
B: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5304
Polymers21,3702
Non-polymers1602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-35 kcal/mol
Surface area8330 Å2
MethodPISA
2
C: Bcl-2 homologous antagonist/killer
D: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4333
Polymers21,3702
Non-polymers641
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-22 kcal/mol
Surface area7860 Å2
MethodPISA
3
E: Bcl-2 homologous antagonist/killer
F: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4333
Polymers21,3702
Non-polymers641
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-28 kcal/mol
Surface area8650 Å2
MethodPISA
4
G: Bcl-2 homologous antagonist/killer
H: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7226
Polymers21,3702
Non-polymers3524
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-45 kcal/mol
Surface area7920 Å2
MethodPISA
5
I: Bcl-2 homologous antagonist/killer
J: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4333
Polymers21,3702
Non-polymers641
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-21 kcal/mol
Surface area8430 Å2
MethodPISA
6
K: Bcl-2 homologous antagonist/killer
L: Bcl-2 homologous antagonist/killer


Theoretical massNumber of molelcules
Total (without water)21,3702
Polymers21,3702
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-25 kcal/mol
Surface area8150 Å2
MethodPISA
7
M: Bcl-2 homologous antagonist/killer
N: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6265
Polymers21,3702
Non-polymers2563
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-47 kcal/mol
Surface area8100 Å2
MethodPISA
8
O: Bcl-2 homologous antagonist/killer
P: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5304
Polymers21,3702
Non-polymers1602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-34 kcal/mol
Surface area8240 Å2
MethodPISA
9
Q: Bcl-2 homologous antagonist/killer
R: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4333
Polymers21,3702
Non-polymers641
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-22 kcal/mol
Surface area8160 Å2
MethodPISA
10
S: Bcl-2 homologous antagonist/killer
T: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5304
Polymers21,3702
Non-polymers1602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-33 kcal/mol
Surface area8360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.385, 132.215, 89.379
Angle α, β, γ (deg.)90.000, 119.200, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 24 or (resid 25 and (name...
21(chain C and (resid 24 or (resid 25 and (name...
31(chain E and (resid 24 or (resid 25 and (name...
41(chain G and (resid 24 through 26 or (resid 27...
51(chain I and (resid 24 or (resid 25 and (name...
61(chain K and (resid 24 or (resid 25 and (name...
71(chain M and (resid 24 or (resid 25 and (name...
81(chain O and (resid 24 or (resid 25 and (name...
91(chain Q and (resid 24 or (resid 25 and (name...
101(chain S and (resid 24 or (resid 25 and (name...
12(chain B and (resid 83 or (resid 84 and (name...
22(chain F and (resid 83 through 84 or (resid 87...
32(chain H and (resid 83 or (resid 84 and (name...
42(chain J and (resid 83 or (resid 84 and (name...
52(chain L and (resid 83 or (resid 84 and (name...
62(chain N and (resid 83 or (resid 84 and (name...
72(chain P and (resid 83 or (resid 84 and (name...
82(chain R and (resid 83 or (resid 84 and (name...
92(chain T and (resid 83 or (resid 84 and (name...

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
111GLUGLUGLUGLU(chain A and (resid 24 or (resid 25 and (name...AA244
121GLUGLUGLUGLU(chain A and (resid 24 or (resid 25 and (name...AA255
131SERSERASNASN(chain A and (resid 24 or (resid 25 and (name...AA23 - 1823 - 162
141SERSERASNASN(chain A and (resid 24 or (resid 25 and (name...AA23 - 1823 - 162
151SERSERASNASN(chain A and (resid 24 or (resid 25 and (name...AA23 - 1823 - 162
161SERSERASNASN(chain A and (resid 24 or (resid 25 and (name...AA23 - 1823 - 162
171SERSERASNASN(chain A and (resid 24 or (resid 25 and (name...AA23 - 1823 - 162
181SERSERASNASN(chain A and (resid 24 or (resid 25 and (name...AA23 - 1823 - 162
191SERSERASNASN(chain A and (resid 24 or (resid 25 and (name...AA23 - 1823 - 162
211GLUGLUGLUGLU(chain C and (resid 24 or (resid 25 and (name...CC244
221GLUGLUGLUGLU(chain C and (resid 24 or (resid 25 and (name...CC255
231SERSERLEULEU(chain C and (resid 24 or (resid 25 and (name...CC23 - 1813 - 161
241SERSERLEULEU(chain C and (resid 24 or (resid 25 and (name...CC23 - 1813 - 161
251SERSERLEULEU(chain C and (resid 24 or (resid 25 and (name...CC23 - 1813 - 161
261SERSERLEULEU(chain C and (resid 24 or (resid 25 and (name...CC23 - 1813 - 161
271SERSERLEULEU(chain C and (resid 24 or (resid 25 and (name...CC23 - 1813 - 161
281SERSERLEULEU(chain C and (resid 24 or (resid 25 and (name...CC23 - 1813 - 161
291SERSERLEULEU(chain C and (resid 24 or (resid 25 and (name...CC23 - 1813 - 161
311GLUGLUGLUGLU(chain E and (resid 24 or (resid 25 and (name...EE244
321GLUGLUGLUGLU(chain E and (resid 24 or (resid 25 and (name...EE255
331ALAALAASNASN(chain E and (resid 24 or (resid 25 and (name...EE22 - 1852 - 165
341ALAALAASNASN(chain E and (resid 24 or (resid 25 and (name...EE22 - 1852 - 165
351ALAALAASNASN(chain E and (resid 24 or (resid 25 and (name...EE22 - 1852 - 165
361ALAALAASNASN(chain E and (resid 24 or (resid 25 and (name...EE22 - 1852 - 165
371ALAALAASNASN(chain E and (resid 24 or (resid 25 and (name...EE22 - 1852 - 165
381ALAALAASNASN(chain E and (resid 24 or (resid 25 and (name...EE22 - 1852 - 165
391ALAALAASNASN(chain E and (resid 24 or (resid 25 and (name...EE22 - 1852 - 165
411GLUGLUGLNGLN(chain G and (resid 24 through 26 or (resid 27...GG24 - 264 - 6
421VALVALVALVAL(chain G and (resid 24 through 26 or (resid 27...GG277
431SERSERLEULEU(chain G and (resid 24 through 26 or (resid 27...GG23 - 1813 - 161
441SERSERLEULEU(chain G and (resid 24 through 26 or (resid 27...GG23 - 1813 - 161
451SERSERLEULEU(chain G and (resid 24 through 26 or (resid 27...GG23 - 1813 - 161
461SERSERLEULEU(chain G and (resid 24 through 26 or (resid 27...GG23 - 1813 - 161
471SERSERLEULEU(chain G and (resid 24 through 26 or (resid 27...GG23 - 1813 - 161
481SERSERLEULEU(chain G and (resid 24 through 26 or (resid 27...GG23 - 1813 - 161
491SERSERLEULEU(chain G and (resid 24 through 26 or (resid 27...GG23 - 1813 - 161
4101SERSERLEULEU(chain G and (resid 24 through 26 or (resid 27...GG23 - 1813 - 161
511GLUGLUGLUGLU(chain I and (resid 24 or (resid 25 and (name...II244
521GLUGLUGLUGLU(chain I and (resid 24 or (resid 25 and (name...II255
531SERSERLEULEU(chain I and (resid 24 or (resid 25 and (name...II21 - 1831 - 163
541SERSERLEULEU(chain I and (resid 24 or (resid 25 and (name...II21 - 1831 - 163
551SERSERLEULEU(chain I and (resid 24 or (resid 25 and (name...II21 - 1831 - 163
561SERSERLEULEU(chain I and (resid 24 or (resid 25 and (name...II21 - 1831 - 163
571SERSERLEULEU(chain I and (resid 24 or (resid 25 and (name...II21 - 1831 - 163
581SERSERLEULEU(chain I and (resid 24 or (resid 25 and (name...II21 - 1831 - 163
591SERSERLEULEU(chain I and (resid 24 or (resid 25 and (name...II21 - 1831 - 163
611GLUGLUGLUGLU(chain K and (resid 24 or (resid 25 and (name...KK244
621GLUGLUGLUGLU(chain K and (resid 24 or (resid 25 and (name...KK255
631SERSERLEULEU(chain K and (resid 24 or (resid 25 and (name...KK23 - 1813 - 161
641SERSERLEULEU(chain K and (resid 24 or (resid 25 and (name...KK23 - 1813 - 161
651SERSERLEULEU(chain K and (resid 24 or (resid 25 and (name...KK23 - 1813 - 161
661SERSERLEULEU(chain K and (resid 24 or (resid 25 and (name...KK23 - 1813 - 161
671SERSERLEULEU(chain K and (resid 24 or (resid 25 and (name...KK23 - 1813 - 161
681SERSERLEULEU(chain K and (resid 24 or (resid 25 and (name...KK23 - 1813 - 161
691SERSERLEULEU(chain K and (resid 24 or (resid 25 and (name...KK23 - 1813 - 161
711GLUGLUGLUGLU(chain M and (resid 24 or (resid 25 and (name...MM244
721GLUGLUGLUGLU(chain M and (resid 24 or (resid 25 and (name...MM255
731SERSERASNASN(chain M and (resid 24 or (resid 25 and (name...MM23 - 1853 - 165
741SERSERASNASN(chain M and (resid 24 or (resid 25 and (name...MM23 - 1853 - 165
751SERSERASNASN(chain M and (resid 24 or (resid 25 and (name...MM23 - 1853 - 165
761SERSERASNASN(chain M and (resid 24 or (resid 25 and (name...MM23 - 1853 - 165
771SERSERASNASN(chain M and (resid 24 or (resid 25 and (name...MM23 - 1853 - 165
781SERSERASNASN(chain M and (resid 24 or (resid 25 and (name...MM23 - 1853 - 165
791SERSERASNASN(chain M and (resid 24 or (resid 25 and (name...MM23 - 1853 - 165
811GLUGLUGLUGLU(chain O and (resid 24 or (resid 25 and (name...OO244
821GLUGLUGLUGLU(chain O and (resid 24 or (resid 25 and (name...OO255
831GLUGLUCYSCYS(chain O and (resid 24 or (resid 25 and (name...OO24 - 1844 - 164
841GLUGLUCYSCYS(chain O and (resid 24 or (resid 25 and (name...OO24 - 1844 - 164
851GLUGLUCYSCYS(chain O and (resid 24 or (resid 25 and (name...OO24 - 1844 - 164
861GLUGLUCYSCYS(chain O and (resid 24 or (resid 25 and (name...OO24 - 1844 - 164
871GLUGLUCYSCYS(chain O and (resid 24 or (resid 25 and (name...OO24 - 1844 - 164
881GLUGLUCYSCYS(chain O and (resid 24 or (resid 25 and (name...OO24 - 1844 - 164
891GLUGLUCYSCYS(chain O and (resid 24 or (resid 25 and (name...OO24 - 1844 - 164
911GLUGLUGLUGLU(chain Q and (resid 24 or (resid 25 and (name...QQ244
921GLUGLUGLUGLU(chain Q and (resid 24 or (resid 25 and (name...QQ255
931SERSERASNASN(chain Q and (resid 24 or (resid 25 and (name...QQ23 - 1823 - 162
941SERSERASNASN(chain Q and (resid 24 or (resid 25 and (name...QQ23 - 1823 - 162
951SERSERASNASN(chain Q and (resid 24 or (resid 25 and (name...QQ23 - 1823 - 162
961SERSERASNASN(chain Q and (resid 24 or (resid 25 and (name...QQ23 - 1823 - 162
971SERSERASNASN(chain Q and (resid 24 or (resid 25 and (name...QQ23 - 1823 - 162
981SERSERASNASN(chain Q and (resid 24 or (resid 25 and (name...QQ23 - 1823 - 162
991SERSERASNASN(chain Q and (resid 24 or (resid 25 and (name...QQ23 - 1823 - 162
1011GLUGLUGLUGLU(chain S and (resid 24 or (resid 25 and (name...SS244
1021GLUGLUGLUGLU(chain S and (resid 24 or (resid 25 and (name...SS255
1031GLUGLUALAALA(chain S and (resid 24 or (resid 25 and (name...SS24 - 1794 - 159
1041GLUGLUALAALA(chain S and (resid 24 or (resid 25 and (name...SS24 - 1794 - 159
1051GLUGLUALAALA(chain S and (resid 24 or (resid 25 and (name...SS24 - 1794 - 159
1061GLUGLUALAALA(chain S and (resid 24 or (resid 25 and (name...SS24 - 1794 - 159
1071GLUGLUALAALA(chain S and (resid 24 or (resid 25 and (name...SS24 - 1794 - 159
1081GLUGLUALAALA(chain S and (resid 24 or (resid 25 and (name...SS24 - 1794 - 159
1091GLUGLUALAALA(chain S and (resid 24 or (resid 25 and (name...SS24 - 1794 - 159
112ASPASPASPASP(chain B and (resid 83 or (resid 84 and (name...BB8316
122ASPASPASPASP(chain B and (resid 83 or (resid 84 and (name...BB8417
132SERSERTYRTYR(chain B and (resid 83 or (resid 84 and (name...BB68 - 891 - 22
142SERSERTYRTYR(chain B and (resid 83 or (resid 84 and (name...BB68 - 891 - 22
152SERSERTYRTYR(chain B and (resid 83 or (resid 84 and (name...BB68 - 891 - 22
162SERSERTYRTYR(chain B and (resid 83 or (resid 84 and (name...BB68 - 891 - 22
172SERSERTYRTYR(chain B and (resid 83 or (resid 84 and (name...BB68 - 891 - 22
182SERSERTYRTYR(chain B and (resid 83 or (resid 84 and (name...BB68 - 891 - 22
212ASPASPASPASP(chain F and (resid 83 through 84 or (resid 87...FF83 - 8416 - 17
222ARGARGARGARG(chain F and (resid 83 through 84 or (resid 87...FF8720
232SERSERCYSCYS(chain F and (resid 83 through 84 or (resid 87...FF69 - 922 - 25
242SERSERCYSCYS(chain F and (resid 83 through 84 or (resid 87...FF69 - 922 - 25
252SERSERCYSCYS(chain F and (resid 83 through 84 or (resid 87...FF69 - 922 - 25
262SERSERCYSCYS(chain F and (resid 83 through 84 or (resid 87...FF69 - 922 - 25
312ASPASPASPASP(chain H and (resid 83 or (resid 84 and (name...HH8316
322ASPASPASPASP(chain H and (resid 83 or (resid 84 and (name...HH8417
332SERSERTYRTYR(chain H and (resid 83 or (resid 84 and (name...HH68 - 891 - 22
342SERSERTYRTYR(chain H and (resid 83 or (resid 84 and (name...HH68 - 891 - 22
352SERSERTYRTYR(chain H and (resid 83 or (resid 84 and (name...HH68 - 891 - 22
362SERSERTYRTYR(chain H and (resid 83 or (resid 84 and (name...HH68 - 891 - 22
372SERSERTYRTYR(chain H and (resid 83 or (resid 84 and (name...HH68 - 891 - 22
382SERSERTYRTYR(chain H and (resid 83 or (resid 84 and (name...HH68 - 891 - 22
412ASPASPASPASP(chain J and (resid 83 or (resid 84 and (name...JJ8316
422ASPASPASPASP(chain J and (resid 83 or (resid 84 and (name...JJ8417
432SERSERARGARG(chain J and (resid 83 or (resid 84 and (name...JJ69 - 882 - 21
442SERSERARGARG(chain J and (resid 83 or (resid 84 and (name...JJ69 - 882 - 21
452SERSERARGARG(chain J and (resid 83 or (resid 84 and (name...JJ69 - 882 - 21
462SERSERARGARG(chain J and (resid 83 or (resid 84 and (name...JJ69 - 882 - 21
472SERSERARGARG(chain J and (resid 83 or (resid 84 and (name...JJ69 - 882 - 21
482SERSERARGARG(chain J and (resid 83 or (resid 84 and (name...JJ69 - 882 - 21
512ASPASPASPASP(chain L and (resid 83 or (resid 84 and (name...LL8316
522ASPASPASPASP(chain L and (resid 83 or (resid 84 and (name...LL8417
532SERSERTYRTYR(chain L and (resid 83 or (resid 84 and (name...LL68 - 891 - 22
542SERSERTYRTYR(chain L and (resid 83 or (resid 84 and (name...LL68 - 891 - 22
552SERSERTYRTYR(chain L and (resid 83 or (resid 84 and (name...LL68 - 891 - 22
562SERSERTYRTYR(chain L and (resid 83 or (resid 84 and (name...LL68 - 891 - 22
572SERSERTYRTYR(chain L and (resid 83 or (resid 84 and (name...LL68 - 891 - 22
582SERSERTYRTYR(chain L and (resid 83 or (resid 84 and (name...LL68 - 891 - 22
612ASPASPASPASP(chain N and (resid 83 or (resid 84 and (name...NN8316
622ASPASPASPASP(chain N and (resid 83 or (resid 84 and (name...NN8417
632METMETTYRTYR(chain N and (resid 83 or (resid 84 and (name...NN71 - 894 - 22
642METMETTYRTYR(chain N and (resid 83 or (resid 84 and (name...NN71 - 894 - 22
652METMETTYRTYR(chain N and (resid 83 or (resid 84 and (name...NN71 - 894 - 22
662METMETTYRTYR(chain N and (resid 83 or (resid 84 and (name...NN71 - 894 - 22
672METMETTYRTYR(chain N and (resid 83 or (resid 84 and (name...NN71 - 894 - 22
682METMETTYRTYR(chain N and (resid 83 or (resid 84 and (name...NN71 - 894 - 22
712ASPASPASPASP(chain P and (resid 83 or (resid 84 and (name...PP8316
722ASPASPASPASP(chain P and (resid 83 or (resid 84 and (name...PP8417
732SERSERTYRTYR(chain P and (resid 83 or (resid 84 and (name...PP68 - 891 - 22
742SERSERTYRTYR(chain P and (resid 83 or (resid 84 and (name...PP68 - 891 - 22
752SERSERTYRTYR(chain P and (resid 83 or (resid 84 and (name...PP68 - 891 - 22
762SERSERTYRTYR(chain P and (resid 83 or (resid 84 and (name...PP68 - 891 - 22
772SERSERTYRTYR(chain P and (resid 83 or (resid 84 and (name...PP68 - 891 - 22
782SERSERTYRTYR(chain P and (resid 83 or (resid 84 and (name...PP68 - 891 - 22
812ASPASPASPASP(chain R and (resid 83 or (resid 84 and (name...RR8316
822ASPASPASPASP(chain R and (resid 83 or (resid 84 and (name...RR8417
832METMETTYRTYR(chain R and (resid 83 or (resid 84 and (name...RR71 - 894 - 22
842METMETTYRTYR(chain R and (resid 83 or (resid 84 and (name...RR71 - 894 - 22
852METMETTYRTYR(chain R and (resid 83 or (resid 84 and (name...RR71 - 894 - 22
862METMETTYRTYR(chain R and (resid 83 or (resid 84 and (name...RR71 - 894 - 22
872METMETTYRTYR(chain R and (resid 83 or (resid 84 and (name...RR71 - 894 - 22
882METMETTYRTYR(chain R and (resid 83 or (resid 84 and (name...RR71 - 894 - 22
912ASPASPASPASP(chain T and (resid 83 or (resid 84 and (name...TT8316
922ASPASPASPASP(chain T and (resid 83 or (resid 84 and (name...TT8417
932SERSERTYRTYR(chain T and (resid 83 or (resid 84 and (name...TT69 - 892 - 22
942SERSERTYRTYR(chain T and (resid 83 or (resid 84 and (name...TT69 - 892 - 22
952SERSERTYRTYR(chain T and (resid 83 or (resid 84 and (name...TT69 - 892 - 22
962SERSERTYRTYR(chain T and (resid 83 or (resid 84 and (name...TT69 - 892 - 22
972SERSERTYRTYR(chain T and (resid 83 or (resid 84 and (name...TT69 - 892 - 22
982SERSERTYRTYR(chain T and (resid 83 or (resid 84 and (name...TT69 - 892 - 22

NCS ensembles :
ID
1
2

-
Components

#1: Protein
Bcl-2 homologous antagonist/killer / Apoptosis regulator BAK / Bcl-2-like protein 7 / Bcl2-L-7


Mass: 18698.918 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAK1, BAK, BCL2L7, CDN1 / Plasmid: pNIC28Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 placI/Y / References: UniProt: Q16611
#2: Protein/peptide
Bcl-2 homologous antagonist/killer / Apoptosis regulator BAK / Bcl-2-like protein 7 / Bcl2-L-7


Mass: 2671.003 Da / Num. of mol.: 10 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16611
#3: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cu
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.84 % / Mosaicity: 0.11 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5 / Details: 0.1 M MES (pH 6.5), 0.5 M Ammonium Sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.06→29.59 Å / Num. obs: 30995 / % possible obs: 91.1 % / Redundancy: 2.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.083 / Rrim(I) all: 0.148 / Net I/σ(I): 7 / Num. measured all: 86262
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.06-3.142.10.596302914580.6040.4870.7741.358.7
13.69-29.5930.04310243410.9950.0290.05222.285.1

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimless0.5.21data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vwz

5vwz


Resolution: 3.06→29.34 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 2028 6.55 %RANDOM
Rwork0.2133 28923 --
obs0.2157 30951 90.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.79 Å2 / Biso mean: 60.6415 Å2 / Biso min: 26.94 Å2
Refinement stepCycle: final / Resolution: 3.06→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13470 0 49 0 13519
Biso mean--79.13 --
Num. residues----1688
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3180X-RAY DIFFRACTION9.581TORSIONAL
12C3180X-RAY DIFFRACTION9.581TORSIONAL
13E3180X-RAY DIFFRACTION9.581TORSIONAL
14G3180X-RAY DIFFRACTION9.581TORSIONAL
15I3180X-RAY DIFFRACTION9.581TORSIONAL
16K3180X-RAY DIFFRACTION9.581TORSIONAL
17M3180X-RAY DIFFRACTION9.581TORSIONAL
18O3180X-RAY DIFFRACTION9.581TORSIONAL
19Q3180X-RAY DIFFRACTION9.581TORSIONAL
110S3180X-RAY DIFFRACTION9.581TORSIONAL
21B63X-RAY DIFFRACTION9.581TORSIONAL
22F63X-RAY DIFFRACTION9.581TORSIONAL
23H63X-RAY DIFFRACTION9.581TORSIONAL
24J63X-RAY DIFFRACTION9.581TORSIONAL
25L63X-RAY DIFFRACTION9.581TORSIONAL
26N63X-RAY DIFFRACTION9.581TORSIONAL
27P63X-RAY DIFFRACTION9.581TORSIONAL
28R63X-RAY DIFFRACTION9.581TORSIONAL
29T63X-RAY DIFFRACTION9.581TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.06-3.140.3445830.31841358144160
3.14-3.230.35491120.29351638175072
3.23-3.320.30881360.27251955209185
3.32-3.430.29361480.25172165231396
3.43-3.550.2621530.22692214236798
3.55-3.690.25221500.22282161231196
3.69-3.860.27541430.23192177232095
3.86-4.060.26291490.21772036218589
4.06-4.320.23221650.18362193235897
4.32-4.650.22751560.1762212236898
4.65-5.110.22121650.18492220238597
5.11-5.850.27131450.2072222236797
5.85-7.350.25961600.22822194235496
7.35-29.340.20361630.19342178234194
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.0475-0.2354-1.5064.55170.32473.9294-0.19950.3878-0.353-0.32490.02910.1275-0.03160.0338-0.00020.36260.0043-0.06240.42460.00020.4891-36.03663.2481-43.399
20.10560.0636-0.07350.3439-0.19330.46670.19260.11591.30010.4310.4897-0.302-0.4375-0.05360.00180.82880.02010.07470.70350.1130.7879-36.52616.9188-46.6526
34.8783-0.6692-2.25384.9590.47573.88210.45250.17160.3932-0.2028-0.1367-0.0076-0.5648-0.11530.02090.4980.03590.07780.29890.04120.4171-20.3019-28.9723-61.1583
40.74060.64540.31741.0436-0.03150.31840.0479-0.1555-0.8842-0.2928-0.4851-0.0192-0.74440.7401-0.00070.43570.00480.10010.50080.02890.4973-23.3309-42.7526-61.58
54.1467-0.1654-0.12084.5718-0.06384.3750.17120.46850.1031-0.3092-0.25840.2608-0.0544-0.1695-0.00020.51210.1138-0.06750.57040.03070.4667-8.2806-31.342917.6934
60.20980.052-0.11110.2221-0.15620.5068-0.0401-0.0194-0.192-0.51780.58480.38451.12090.07870.00430.86760.0324-0.1550.8683-0.06670.7308-10.0731-45.043820.6752
73.63420.71690.39024.84730.93292.96690.0280.3583-0.1586-0.14220.0401-0.17330.2035-0.40210.00030.611-0.0213-0.04650.71260.05510.503326.97692.23275.1143
80.9237-0.45460.81790.2695-0.44340.9105-1.45420.350.4633-0.5770.3452-1.5341-1.3780.1934-0.11980.9572-0.1249-0.08560.63250.11670.802231.082114.99132.991
92.82930.50231.40935.46430.70053.1528-0.0815-0.3983-0.01060.38090.132-0.00230.0407-0.2336-0.00020.36480.02110.05610.3731-0.00570.3374-13.40421.3226-18.2518
100.7027-0.56130.14471.1494-0.41810.1659-0.6692-0.38720.06670.1449-0.36830.1896-0.87680.2666-0.0010.51240.03680.02790.4046-0.07540.5222-16.508814.8593-19.5057
113.5260.03510.94564.2796-0.2182.9073-0.0081-0.0118-0.2597-0.17360.0896-0.12410.06790.1966-0.00020.3599-0.01010.0560.3434-0.01110.4216-9.455-25.0644-28.4847
122.52631.614-0.87662.1185-1.67141.4285-0.01920.1865-2.1306-0.6101-0.5516-0.34661.08080.194-0.43440.66960.17120.01050.6258-0.09040.7462-9.1893-38.7618-32.7561
136.22940.3928-1.45843.8266-0.92872.3941-0.0362-0.2032-0.11980.1128-0.2037-0.1066-0.06190.035900.36360.0101-0.06930.3233-0.01120.366518.62090.9591-31.9797
140.4731-0.0631-0.520.79470.2070.58250.27240.09511.73250.731-0.7440.22710.2309-0.2348-0.00670.60170.0529-0.12620.5852-0.01470.680217.200314.8656-29.0539
153.76680.4487-0.00694.2452-0.26383.2815-0.06280.00360.4362-0.03630.08560.1425-0.222-0.5902-0.00010.37620.0246-0.01350.47150.00230.44825.8554-30.2608-28.296
160.239-0.57260.17891.28-0.31540.2719-0.1374-1.3411-0.26220.3281-0.02790.1976-0.11790.2691-0.00020.4451-0.0805-0.06380.52440.05460.416328.1916-42.7874-23.4151
173.09940.2263-1.3544.99070.46385.22780.2154-0.3657-0.00640.0761-0.1655-0.1417-0.44830.4773-0.00010.4609-0.06530.00620.42280.00460.3793-37.1504-27.1933-7.7613
180.4969-0.3456-0.22460.7008-0.13290.1948-0.4708-0.0133-0.5024-0.3376-0.1072-0.70651.38590.9851-0.0050.60510.0420.04330.86420.08630.8257-31.7683-40.3141-8.2273
191.9961-0.71-0.27723.50630.45433.8754-0.04910.126-0.1122-0.119-0.12940.13890.26480.111-0.00010.49460.0306-0.01760.4340.03380.3687-28.97992.188112.3241
200.43330.31310.41580.57640.66610.80810.64040.28130.2257-0.0718-0.2275-0.8605-1.58690.62770.00770.5759-0.01180.03860.62950.00410.5807-26.883415.424516.3579
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'M' and resid 23 through 185)M23 - 185
2X-RAY DIFFRACTION2(chain 'N' and resid 71 through 89)N71 - 89
3X-RAY DIFFRACTION3(chain 'O' and resid 24 through 184)O24 - 184
4X-RAY DIFFRACTION4(chain 'P' and resid 68 through 89)P68 - 89
5X-RAY DIFFRACTION5(chain 'Q' and resid 23 through 182)Q23 - 182
6X-RAY DIFFRACTION6(chain 'R' and resid 71 through 89)R71 - 89
7X-RAY DIFFRACTION7(chain 'S' and resid 24 through 179)S24 - 179
8X-RAY DIFFRACTION8(chain 'T' and resid 69 through 89)T69 - 89
9X-RAY DIFFRACTION9(chain 'A' and resid 23 through 182)A23 - 182
10X-RAY DIFFRACTION10(chain 'B' and resid 68 through 89)B68 - 89
11X-RAY DIFFRACTION11(chain 'C' and resid 23 through 181)C23 - 181
12X-RAY DIFFRACTION12(chain 'D' and resid 70 through 86)D70 - 86
13X-RAY DIFFRACTION13(chain 'E' and resid 22 through 185)E22 - 185
14X-RAY DIFFRACTION14(chain 'F' and resid 69 through 92)F69 - 92
15X-RAY DIFFRACTION15(chain 'G' and resid 23 through 181)G23 - 181
16X-RAY DIFFRACTION16(chain 'H' and resid 68 through 89)H68 - 89
17X-RAY DIFFRACTION17(chain 'I' and resid 21 through 183)I21 - 183
18X-RAY DIFFRACTION18(chain 'J' and resid 69 through 88)J69 - 88
19X-RAY DIFFRACTION19(chain 'K' and resid 23 through 181)K23 - 181
20X-RAY DIFFRACTION20(chain 'L' and resid 68 through 89)L68 - 89

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