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- PDB-2g5b: Crystal Structure of the anti-Bax monoclonal antibody 6A7 and a B... -

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Basic information

Entry
Database: PDB / ID: 2g5b
TitleCrystal Structure of the anti-Bax monoclonal antibody 6A7 and a Bax peptide.
Components
  • 6A7 Fab Heavy Chain
  • 6A7 Fab Light Chain
  • Bax Peptide
KeywordsAPOPTOSIS / 6A7 / Bax / Fab / Antibody / Fab-Peptide Complex
Function / homology
Function and homology information


positive regulation of reproductive process / T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / BAX complex / protein insertion into mitochondrial membrane / B cell receptor apoptotic signaling pathway / positive regulation of motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / Activation, translocation and oligomerization of BAX ...positive regulation of reproductive process / T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / BAX complex / protein insertion into mitochondrial membrane / B cell receptor apoptotic signaling pathway / positive regulation of motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / Activation, translocation and oligomerization of BAX / spermatid differentiation / Sertoli cell proliferation / NTRK3 as a dependence receptor / positive regulation of apoptotic DNA fragmentation / development of secondary sexual characteristics / positive regulation of B cell apoptotic process / positive regulation of mitochondrial membrane permeability involved in apoptotic process / B cell homeostatic proliferation / glycosphingolipid metabolic process / apoptotic process involved in mammary gland involution / retinal cell programmed cell death / B cell negative selection / BAK complex / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / negative regulation of endoplasmic reticulum calcium ion concentration / apoptotic process involved in embryonic digit morphogenesis / mitochondrial permeability transition pore complex / Release of apoptotic factors from the mitochondria / mitochondrial fragmentation involved in apoptotic process / post-embryonic camera-type eye morphogenesis / apoptotic process involved in blood vessel morphogenesis / Transcriptional regulation by RUNX2 / establishment or maintenance of transmembrane electrochemical gradient / positive regulation of apoptotic process involved in mammary gland involution / regulation of nitrogen utilization / B cell apoptotic process / endoplasmic reticulum calcium ion homeostasis / calcium ion transport into cytosol / fertilization / epithelial cell apoptotic process / positive regulation of epithelial cell apoptotic process / Bcl-2 family protein complex / mitochondrial fusion / motor neuron apoptotic process / myeloid cell homeostasis / execution phase of apoptosis / thymocyte apoptotic process / positive regulation of IRE1-mediated unfolded protein response / hypothalamus development / pore complex / odontogenesis of dentin-containing tooth / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / germ cell development / immunoglobulin mediated immune response / vagina development / positive regulation of release of cytochrome c from mitochondria / B cell homeostasis / apoptotic mitochondrial changes / negative regulation of mitochondrial membrane potential / intrinsic apoptotic signaling pathway by p53 class mediator / BH3 domain binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / negative regulation of apoptotic signaling pathway / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of calcium ion transport into cytosol / cellular response to unfolded protein / Pyroptosis / negative regulation of protein binding / blood vessel remodeling / immunoglobulin complex / ectopic germ cell programmed cell death / response to axon injury / antigen binding / ovarian follicle development / negative regulation of fibroblast proliferation / extrinsic apoptotic signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / supramolecular fiber organization / response to salt stress / extrinsic apoptotic signaling pathway in absence of ligand / release of sequestered calcium ion into cytosol / homeostasis of number of cells within a tissue / Hsp70 protein binding / intrinsic apoptotic signaling pathway / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of release of sequestered calcium ion into cytosol / regulation of mitochondrial membrane potential / response to gamma radiation / apoptotic signaling pathway / kidney development / positive regulation of protein-containing complex assembly / cerebral cortex development / cellular response to virus / response to toxic substance / neuron migration / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / nuclear envelope / positive regulation of neuron apoptotic process
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-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / 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-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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig heavy chain Mem5 / Apoptosis regulator BAX / :
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPeyerl, F.W. / Dai, S. / Murphy, G.A. / Marrack, P. / Kappler, J.W.
CitationJournal: Cell Death Differ. / Year: 2007
Title: Elucidation of some Bax conformational changes through crystallization of an antibody-peptide complex.
Authors: Peyerl, F.W. / Dai, S. / Murphy, G.A. / Crawford, F. / White, J. / Marrack, P. / Kappler, J.W.
History
DepositionFeb 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE There is no suitable sequence database reference available.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6A7 Fab Light Chain
B: 6A7 Fab Heavy Chain
C: 6A7 Fab Light Chain
D: 6A7 Fab Heavy Chain
E: 6A7 Fab Light Chain
F: 6A7 Fab Heavy Chain
G: 6A7 Fab Light Chain
H: 6A7 Fab Heavy Chain
I: Bax Peptide
J: Bax Peptide
K: Bax Peptide
L: Bax Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,96123
Polymers195,10512
Non-polymers2,85611
Water7,602422
1
A: 6A7 Fab Light Chain
B: 6A7 Fab Heavy Chain
I: Bax Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5556
Polymers48,7763
Non-polymers7793
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 6A7 Fab Light Chain
D: 6A7 Fab Heavy Chain
J: Bax Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3936
Polymers48,7763
Non-polymers6173
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 6A7 Fab Light Chain
F: 6A7 Fab Heavy Chain
K: Bax Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5556
Polymers48,7763
Non-polymers7793
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: 6A7 Fab Light Chain
H: 6A7 Fab Heavy Chain
L: Bax Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4595
Polymers48,7763
Non-polymers6832
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.528, 183.897, 67.081
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein/peptide , 1 types, 4 molecules IJKL

#3: Protein/peptide
Bax Peptide


Mass: 760.790 Da / Num. of mol.: 4 / Fragment: Bax peptide fragment / Source method: obtained synthetically / Details: This sequence occurs naturally in mice and humans / References: UniProt: Q07812*PLUS

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Antibody , 2 types, 8 molecules ACEGBDFH

#1: Antibody
6A7 Fab Light Chain


Mass: 24086.699 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) / References: UniProt: Q58EU4
#2: Antibody
6A7 Fab Heavy Chain


Mass: 23928.721 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) / References: UniProt: P84751

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Sugars , 3 types, 4 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 429 molecules

#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.35
Details: 20% PEG 8000, 0.1 M Tris-HCl, pH 7.35, 0.4 M lithium sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→49.58 Å / Num. all: 106760 / Num. obs: 91909 / % possible obs: 99.9 % / Observed criterion σ(I): 5 / Redundancy: 5.71 % / Rmerge(I) obs: 0.106
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.68 % / Rmerge(I) obs: 0.63 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
CNS1refinement
PDB_EXTRACT1.701data extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 4606 5 %Random
Rwork0.234 ---
all-91909 --
obs-88303 99.6 %-
Solvent computationBsol: 25.899 Å2
Displacement parametersBiso mean: 42.683 Å2
Baniso -1Baniso -2Baniso -3
1--5.715 Å20 Å20 Å2
2--6.315 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13596 0 180 422 14198
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param

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