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- PDB-5w5x: Crystal structure of BAXP168G in complex with an activating antibody -

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Basic information

Entry
Database: PDB / ID: 5w5x
TitleCrystal structure of BAXP168G in complex with an activating antibody
Components
  • 3C10 Fab' heavy chain
  • 3C10 Fab' light chain
  • Apoptosis regulator BAX
KeywordsAPOPTOSIS/IMMUNE SYSTEM / Fab' / BAX activation / unfolding / APOPTOSIS / APOPTOSIS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / protein insertion into mitochondrial membrane / BAX complex / B cell receptor apoptotic signaling pathway / positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / spermatid differentiation ...T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / protein insertion into mitochondrial membrane / BAX complex / B cell receptor apoptotic signaling pathway / positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / spermatid differentiation / Activation, translocation and oligomerization of BAX / positive regulation of B cell apoptotic process / development of secondary sexual characteristics / NTRK3 as a dependence receptor / Sertoli cell proliferation / positive regulation of apoptotic DNA fragmentation / B cell homeostatic proliferation / glycosphingolipid metabolic process / positive regulation of mitochondrial membrane permeability involved in apoptotic process / retinal cell programmed cell death / B cell negative selection / BAK complex / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / apoptotic process involved in blood vessel morphogenesis / mitochondrial fragmentation involved in apoptotic process / negative regulation of endoplasmic reticulum calcium ion concentration / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / apoptotic process involved in embryonic digit morphogenesis / mitochondrial permeability transition pore complex / Release of apoptotic factors from the mitochondria / post-embryonic camera-type eye morphogenesis / establishment or maintenance of transmembrane electrochemical gradient / apoptotic process involved in mammary gland involution / Transcriptional regulation by RUNX2 / positive regulation of apoptotic process involved in mammary gland involution / regulation of nitrogen utilization / B cell apoptotic process / endoplasmic reticulum calcium ion homeostasis / positive regulation of endoplasmic reticulum unfolded protein response / fertilization / calcium ion transport into cytosol / motor neuron apoptotic process / mitochondrial fusion / channel activity / positive regulation of epithelial cell apoptotic process / Bcl-2 family protein complex / epithelial cell apoptotic process / myeloid cell homeostasis / hypothalamus development / positive regulation of calcium ion transport into cytosol / thymocyte apoptotic process / pore complex / BH3 domain binding / germ cell development / odontogenesis of dentin-containing tooth / apoptotic mitochondrial changes / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / negative regulation of mitochondrial membrane potential / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / vagina development / B cell homeostasis / negative regulation of apoptotic signaling pathway / intrinsic apoptotic signaling pathway by p53 class mediator / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / response to axon injury / ectopic germ cell programmed cell death / cellular response to unfolded protein / blood vessel remodeling / Pyroptosis / supramolecular fiber organization / negative regulation of peptidyl-serine phosphorylation / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / homeostasis of number of cells within a tissue / extrinsic apoptotic signaling pathway / ovarian follicle development / release of sequestered calcium ion into cytosol / extrinsic apoptotic signaling pathway in absence of ligand / response to salt stress / Hsp70 protein binding / intrinsic apoptotic signaling pathway / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of release of sequestered calcium ion into cytosol / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / negative regulation of protein binding / kidney development / positive regulation of protein-containing complex assembly / apoptotic signaling pathway / response to gamma radiation / neuron migration / response to toxic substance / cerebral cortex development / cellular response to virus / activation of cysteine-type endopeptidase activity involved in apoptotic process / cellular response to UV / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process
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 (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family ...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 (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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Apoptosis regulator BAX
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å
AuthorsRobin, A.Y. / Colman, P.M. / Czabotar, P.E.
CitationJournal: Structure / Year: 2018
Title: Ensemble Properties of Bax Determine Its Function.
Authors: Robin, A.Y. / Iyer, S. / Birkinshaw, R.W. / Sandow, J. / Wardak, A. / Luo, C.S. / Shi, M. / Webb, A.I. / Czabotar, P.E. / Kluck, R.M. / Colman, P.M.
History
DepositionJun 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 17, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 2.0Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: 3C10 Fab' light chain
H: 3C10 Fab' heavy chain
A: Apoptosis regulator BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,30413
Polymers69,6803
Non-polymers62410
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-40 kcal/mol
Surface area26260 Å2
MethodPISA
2
L: 3C10 Fab' light chain
H: 3C10 Fab' heavy chain
A: Apoptosis regulator BAX
hetero molecules

L: 3C10 Fab' light chain
H: 3C10 Fab' heavy chain
A: Apoptosis regulator BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,60926
Polymers139,3616
Non-polymers1,24820
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area13270 Å2
ΔGint-86 kcal/mol
Surface area52010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.309, 68.309, 288.643
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11L-307-

ZN

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Components

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Protein , 1 types, 1 molecules A

#3: Protein Apoptosis regulator BAX / Bcl-2-like protein 4 / Bcl2-L-4


Mass: 21306.316 Da / Num. of mol.: 1 / Mutation: C62S C126S P168G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAX, BCL2L4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07812

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Antibody , 2 types, 2 molecules LH

#1: Antibody 3C10 Fab' light chain


Mass: 23457.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
#2: Antibody 3C10 Fab' heavy chain


Mass: 24917.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: N-terminus glutamate is converted into a pyroglutamate residue. C-terminus residues not seen in structure.
Source: (natural) Rattus norvegicus (Norway rat)

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Non-polymers , 3 types, 108 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.502→47.639 Å / Num. obs: 24112 / % possible obs: 97 % / Redundancy: 5.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1018 / Net I/σ(I): 13.37
Reflection shellHighest resolution: 2.502 Å / Rmerge(I) obs: 0.9118 / CC1/2: 0.558

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZAN

1zan


Resolution: 2.502→47.639 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.62
RfactorNum. reflection% reflection
Rfree0.2435 1204 4.99 %
Rwork0.1871 --
obs0.1899 24112 97.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.502→47.639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4442 0 37 98 4577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034572
X-RAY DIFFRACTIONf_angle_d0.5936212
X-RAY DIFFRACTIONf_dihedral_angle_d13.9582678
X-RAY DIFFRACTIONf_chiral_restr0.042716
X-RAY DIFFRACTIONf_plane_restr0.004784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5016-2.60170.34451320.28152518X-RAY DIFFRACTION98
2.6017-2.72010.32111330.2612509X-RAY DIFFRACTION99
2.7201-2.86350.31811360.23952541X-RAY DIFFRACTION99
2.8635-3.04290.29981340.22082528X-RAY DIFFRACTION99
3.0429-3.27780.27111310.20092546X-RAY DIFFRACTION98
3.2778-3.60750.24281310.18572537X-RAY DIFFRACTION98
3.6075-4.12930.22981300.16222526X-RAY DIFFRACTION97
4.1293-5.20140.18071360.14672560X-RAY DIFFRACTION96
5.2014-47.6480.231410.1822643X-RAY DIFFRACTION93
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)
11.95580.6779-0.39951.5638-0.47111.99350.1786-0.2559-0.1330.1627-0.1312-0.00110.2092-0.0243-0.0360.2513-0.023-0.04270.32640.00870.302-33.483-22.8092-22.6287
21.78080.36120.61732.24410.85854.31460.0762-0.29980.10840.0883-0.28960.2046-0.336-0.61360.16720.3261-0.0135-0.03140.3672-0.03280.3304-15.20076.1562-12.5405
33.90490.6820.13656.23970.72353.08220.1781-0.06890.14580.0796-0.1622-0.5929-0.00190.4066-0.01690.3614-0.06530.01120.44970.08340.4884-54.8691-51.1524-25.097
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain H and resid 1:117 or chain L and resid 1:109 or chain A and resid 31:45
2X-RAY DIFFRACTION2chain H and resid 118:212 or chain L and resid 110:214
3X-RAY DIFFRACTION3chain A and resid 1:30 or chain A and resid 46:200

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