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- PDB-7lk4: Crystal structure of BAK L100A in complex with activating antibod... -

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Basic information

Entry
Database: PDB / ID: 7lk4
TitleCrystal structure of BAK L100A in complex with activating antibody fragments
Components
  • 7D10 antibody VH fragment
  • 7D10 antibody VL fragment
  • Bcl-2 homologous antagonist/killer
KeywordsAPOPTOSIS / swap dimer / antibody fragments
Function / homology
Function and homology information


Activation and oligomerization of BAK protein / BH domain binding / B cell negative selection / BAK complex / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / response to mycotoxin / limb morphogenesis / Release of apoptotic factors from the mitochondria / apoptotic process involved in blood vessel morphogenesis ...Activation and oligomerization of BAK protein / BH domain binding / B cell negative selection / BAK complex / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / response to mycotoxin / limb morphogenesis / Release of apoptotic factors from the mitochondria / apoptotic process involved in blood vessel morphogenesis / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / establishment or maintenance of transmembrane electrochemical gradient / B cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / endoplasmic reticulum calcium ion homeostasis / regulation of mitochondrial membrane permeability / calcium ion transport into cytosol / fibroblast apoptotic process / response to UV-C / mitochondrial fusion / Bcl-2 family protein complex / myeloid cell homeostasis / 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 / vagina development / B cell homeostasis / positive regulation of calcium ion transport into cytosol / positive regulation of proteolysis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / blood vessel remodeling / animal organ regeneration / cellular response to unfolded protein / Pyroptosis / heat shock protein binding / extrinsic apoptotic signaling pathway in absence of ligand / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / epithelial cell proliferation / response to gamma radiation / regulation of mitochondrial membrane potential / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / response to hydrogen peroxide / establishment of localization in cell / cellular response to mechanical stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / protein-folding chaperone binding / channel activity / response to ethanol / transmembrane transporter binding / mitochondrial outer membrane / regulation of cell cycle / positive regulation of apoptotic process / response to xenobiotic stimulus / 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 / metal ion binding / identical protein binding / cytosol
Similarity search - Function
Blc2-like / Apoptosis Regulator Bcl-x / 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-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions ...Blc2-like / Apoptosis Regulator Bcl-x / 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-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsRobin, Y.A. / Colman, P.M.
CitationJournal: Cell Death Differ. / Year: 2022
Title: Structure of the BAK-activating antibody 7D10 bound to BAK reveals an unexpected role for the alpha 1-alpha 2 loop in BAK activation.
Authors: Robin, A.Y. / Miller, M.S. / Iyer, S. / Shi, M.X. / Wardak, A.Z. / Lio, D. / Smith, N.A. / Smith, B.J. / Birkinshaw, R.W. / Czabotar, P.E. / Kluck, R.M. / Colman, P.M.
History
DepositionFeb 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: Bcl-2 homologous antagonist/killer
Q: Bcl-2 homologous antagonist/killer
R: Bcl-2 homologous antagonist/killer
S: Bcl-2 homologous antagonist/killer
A: 7D10 antibody VL fragment
B: 7D10 antibody VH fragment
C: 7D10 antibody VL fragment
D: 7D10 antibody VH fragment
E: 7D10 antibody VL fragment
F: 7D10 antibody VH fragment
G: 7D10 antibody VL fragment
H: 7D10 antibody VH fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,60419
Polymers177,77712
Non-polymers8277
Water32418
1
P: Bcl-2 homologous antagonist/killer
R: Bcl-2 homologous antagonist/killer
A: 7D10 antibody VL fragment
B: 7D10 antibody VH fragment
E: 7D10 antibody VL fragment
F: 7D10 antibody VH fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,2439
Polymers88,8896
Non-polymers3553
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
Q: Bcl-2 homologous antagonist/killer
S: Bcl-2 homologous antagonist/killer
C: 7D10 antibody VL fragment
D: 7D10 antibody VH fragment
G: 7D10 antibody VL fragment
H: 7D10 antibody VH fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,36110
Polymers88,8896
Non-polymers4734
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.170, 271.800, 74.040
Angle α, β, γ (deg.)90.000, 91.790, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and (resid 1 through 88 or resid 90 through 120))
21(chain D and (resid 1 through 88 or resid 90 through 120))
31(chain F and (resid 1 through 88 or resid 90 through 120))
41(chain H and (resid 1 through 88 or resid 90 through 120))
12chain A
22chain C
32chain E
42chain G
13(chain P and (resid 23 through 31 or (resid 32...
23(chain Q and (resid 23 through 31 or (resid 32...
33(chain R and (resid 23 through 36 or resid 38...

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
111GLUGLUSERSER(chain B and (resid 1 through 88 or resid 90 through 120))BF1 - 883 - 90
121ASPASPGLYGLY(chain B and (resid 1 through 88 or resid 90 through 120))BF90 - 12092 - 122
211GLUGLUSERSER(chain D and (resid 1 through 88 or resid 90 through 120))DH1 - 883 - 90
221ASPASPGLYGLY(chain D and (resid 1 through 88 or resid 90 through 120))DH90 - 12092 - 122
311GLUGLUSERSER(chain F and (resid 1 through 88 or resid 90 through 120))FJ1 - 883 - 90
321ASPASPGLYGLY(chain F and (resid 1 through 88 or resid 90 through 120))FJ90 - 12092 - 122
411GLUGLUSERSER(chain H and (resid 1 through 88 or resid 90 through 120))HL1 - 883 - 90
421ASPASPGLYGLY(chain H and (resid 1 through 88 or resid 90 through 120))HL90 - 12092 - 122
112GLYGLYLYSLYSchain AAE-1 - 1071 - 109
212GLYGLYLYSLYSchain CCG-1 - 1071 - 109
312GLYGLYLYSLYSchain EEI-1 - 1071 - 109
412GLYGLYLYSLYSchain GGK-1 - 1071 - 109
113SERSERTHRTHR(chain P and (resid 23 through 31 or (resid 32...PA23 - 311 - 9
123GLUGLUGLUGLU(chain P and (resid 23 through 31 or (resid 32...PA3210
133SERSERASNASN(chain P and (resid 23 through 31 or (resid 32...PA23 - 1821 - 160
143SERSERASNASN(chain P and (resid 23 through 31 or (resid 32...PA23 - 1821 - 160
153SERSERASNASN(chain P and (resid 23 through 31 or (resid 32...PA23 - 1821 - 160
163SERSERASNASN(chain P and (resid 23 through 31 or (resid 32...PA23 - 1821 - 160
213SERSERTHRTHR(chain Q and (resid 23 through 31 or (resid 32...QB23 - 311 - 9
223GLUGLUGLUGLU(chain Q and (resid 23 through 31 or (resid 32...QB3210
233SERSERASNASN(chain Q and (resid 23 through 31 or (resid 32...QB23 - 1821 - 160
243SERSERASNASN(chain Q and (resid 23 through 31 or (resid 32...QB23 - 1821 - 160
253SERSERASNASN(chain Q and (resid 23 through 31 or (resid 32...QB23 - 1821 - 160
263SERSERASNASN(chain Q and (resid 23 through 31 or (resid 32...QB23 - 1821 - 160
313SERSERARGARG(chain R and (resid 23 through 36 or resid 38...RC23 - 361 - 14
323TYRTYRPROPRO(chain R and (resid 23 through 36 or resid 38...RC38 - 5816 - 36
333SERSERILEILE(chain R and (resid 23 through 36 or resid 38...RC69 - 8047 - 58
343HISHISALAALA(chain R and (resid 23 through 36 or resid 38...RC99 - 10077 - 78
353GLNGLNGLNGLN(chain R and (resid 23 through 36 or resid 38...RC10179
363SERSERALAALA(chain R and (resid 23 through 36 or resid 38...RC23 - 1791 - 157
373SERSERALAALA(chain R and (resid 23 through 36 or resid 38...RC23 - 1791 - 157
383SERSERALAALA(chain R and (resid 23 through 36 or resid 38...RC23 - 1791 - 157
393SERSERALAALA(chain R and (resid 23 through 36 or resid 38...RC23 - 1791 - 157

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 18452.590 Da / Num. of mol.: 4 / Mutation: L100A, C166S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAK1, BAK, BCL2L7, CDN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16611
#2: Antibody
7D10 antibody VL fragment


Mass: 11728.907 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Brevibacillus brevis (bacteria)
#3: Antibody
7D10 antibody VH fragment


Mass: 14262.789 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Brevibacillus brevis (bacteria)
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.97 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 38.9 % 2-methyl-2,4-pentanediol, 0.1 M Sodium cacodylate pH 6.44, 4 % Polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.1→39.385 Å / Num. obs: 40131 / % possible obs: 98.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 66.95 Å2 / CC1/2: 0.98 / Net I/σ(I): 6.8
Reflection shellResolution: 3.1→3.21 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3207 / CC1/2: 0.43 / % possible all: 98.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
PHASERphasing
PDB_EXTRACT3.27data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W5X

5w5x


Resolution: 3.1→39.385 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2621 1711 4.26 %
Rwork0.2144 38420 -
obs0.2164 40131 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 301.22 Å2 / Biso mean: 85.1927 Å2 / Biso min: 16.56 Å2
Refinement stepCycle: final / Resolution: 3.1→39.385 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11533 0 56 18 11607
Biso mean--73.41 30.05 -
Num. residues----1500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211896
X-RAY DIFFRACTIONf_angle_d0.50216160
X-RAY DIFFRACTIONf_dihedral_angle_d16.0226915
X-RAY DIFFRACTIONf_chiral_restr0.0381763
X-RAY DIFFRACTIONf_plane_restr0.0032077
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B1987X-RAY DIFFRACTION11.047TORSIONAL
12D1987X-RAY DIFFRACTION11.047TORSIONAL
13F1987X-RAY DIFFRACTION11.047TORSIONAL
14H1987X-RAY DIFFRACTION11.047TORSIONAL
21A2195X-RAY DIFFRACTION11.047TORSIONAL
22C2195X-RAY DIFFRACTION11.047TORSIONAL
23E2195X-RAY DIFFRACTION11.047TORSIONAL
24G2195X-RAY DIFFRACTION11.047TORSIONAL
31P1693X-RAY DIFFRACTION11.047TORSIONAL
32Q1693X-RAY DIFFRACTION11.047TORSIONAL
33R1693X-RAY DIFFRACTION11.047TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1001-3.19120.35681480.3257320798
3.1912-3.29420.35571390.3049313598
3.2942-3.41190.36091420.2862320098
3.4119-3.54840.28321390.2476321198
3.5484-3.70980.29381470.2358315799
3.7098-3.90520.27431330.2241321699
3.9052-4.14960.24851470.2142318298
4.1496-4.46960.21991480.1794320199
4.4696-4.91870.22811460.1669320098
4.9187-5.62860.22571300.1936323899
5.6286-7.08470.27881460.2247322199
7.0847-39.3850.22851460.1825325299
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)
11.58440.267-0.13284.2256-1.94351.92330.03540.02040.31680.04920.0380.154-0.41330.097-0.03460.6848-0.05920.03850.4554-0.080.3227-8.726854.650745.0183
21.876-0.58950.29411.57650.25130.6995-0.003-0.16480.5705-0.0149-0.085-0.1582-0.2401-0.01460.0470.6483-0.0370.11750.44470.02420.473-1.845954.853320.3446
31.83321.32090.51843.92190.59821.42890.08270.0119-0.436-0.0170.074-0.37340.2307-0.0782-0.09550.4255-0.01430.06060.4610.06630.3692-22.4172130.899736.7757
43.2123-0.8657-1.07971.2665-0.31531.59390.0729-0.0249-0.2045-0.0212-0.1070.00830.0256-0.00510.05430.5187-0.0356-0.06110.3664-0.04810.2693-28.8944143.9114.9957
50.5968-1.0884-1.18456.11810.25043.2371-0.5653-0.22040.8605-0.57880.609-0.03950.49530.07-0.07850.7410.0452-0.2080.4060.02371.0486-11.313871.756831.6178
65.5304-2.3838-0.09776.6273-0.23832.8848-0.0244-0.6118-0.1617-0.50480.19760.23360.0887-0.3155-0.15620.6651-0.00820.06010.51360.06431.2083-24.0076108.270624.3385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'P' and (resid 49 through 58 ) or chain 'E' or chain 'F'P0
2X-RAY DIFFRACTION2chain 'R' and (resid 49 through 60) or chain 'A' or chain 'B'R0
3X-RAY DIFFRACTION3chain 'Q' and (resid 49 through 60) or chain 'G' or chain 'H'Q0
4X-RAY DIFFRACTION4chain 'S' and (resid 49 through 61) or chain 'C' or chain 'D'S0
5X-RAY DIFFRACTION5chain 'P' and (not (resid 49 through 61)) or chain 'R' and (not (resid 49 through 61))P0
6X-RAY DIFFRACTION6chain 'Q' and (not (resid 49 through 61)) or chain 'S' and (not (resid 49 through 61))Q0

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