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- PDB-7st8: Crystal structure of 7H2.2 Fab in complex with SAS1B C-terminal region -

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Basic information

Entry
Database: PDB / ID: 7st8
TitleCrystal structure of 7H2.2 Fab in complex with SAS1B C-terminal region
Components
  • 7H2.2 Fab Heavy Chain
  • 7H2.2 Fab Light Chain
  • Astacin-like metalloendopeptidase
KeywordsIMMUNE SYSTEM / Cancer / antibody / oocyte antigen
Function / homology
Function and homology information


glutamic-type peptidase activity / negative regulation of binding of sperm to zona pellucida / aspartic-type peptidase activity / prevention of polyspermy / cortical granule / positive regulation of protein processing / fertilization / Hydrolases; Acting on peptide bonds (peptidases) / metalloendopeptidase activity / cell adhesion ...glutamic-type peptidase activity / negative regulation of binding of sperm to zona pellucida / aspartic-type peptidase activity / prevention of polyspermy / cortical granule / positive regulation of protein processing / fertilization / Hydrolases; Acting on peptide bonds (peptidases) / metalloendopeptidase activity / cell adhesion / zinc ion binding / plasma membrane / cytoplasm
Similarity search - Function
Astacin-like domain profile. / Peptidase M12A / Astacin (Peptidase family M12A) / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Astacin-like metalloendopeptidase
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsLegg, M.S.G. / Evans, S.V.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)499037-16 Canada
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2022
Title: Monoclonal antibody 7H2.2 binds the C-terminus of the cancer-oocyte antigen SAS1B through the hydrophilic face of a conserved amphipathic helix corresponding to one of only two regions predicted to be ordered
Authors: Legg, M.S.G. / Gagnon, S.M.L. / Powell, C.J. / Boulanger, M.J. / Li, A.J.J. / Evans, S.V.
History
DepositionNov 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: 7H2.2 Fab Heavy Chain
L: 7H2.2 Fab Light Chain
S: Astacin-like metalloendopeptidase


Theoretical massNumber of molelcules
Total (without water)64,9003
Polymers64,9003
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-33 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.355, 43.030, 106.227
Angle α, β, γ (deg.)90.000, 123.890, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody 7H2.2 Fab Heavy Chain


Mass: 23838.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody 7H2.2 Fab Light Chain


Mass: 23852.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Protein Astacin-like metalloendopeptidase / SAS1B / Oocyte astacin / Ovastacin / ZP2-proteinase


Mass: 17208.973 Da / Num. of mol.: 1 / Fragment: C-terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASTL / Production host: Escherichia coli (E. coli)
References: UniProt: Q6HA08, Hydrolases; Acting on peptide bonds (peptidases)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 1.93 Å3/Da / Density % sol: 36.42 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M CHES, pH 9.5, 20 % (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→40 Å / Num. obs: 13315 / % possible obs: 96.9 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.049 / Rrim(I) all: 0.169 / Χ2: 1.146 / Net I/σ(I): 16.9 / Num. measured all: 129654
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.854.60.50312850.8720.2460.5641.11194.9
2.85-2.965.40.43212950.9280.190.4751.10295.6
2.96-3.16.80.35512840.9270.1410.3841.10593.2
3.1-3.2680.28612840.9580.1010.3051.07296
3.26-3.468.60.2913210.9260.0980.3081.43596.4
3.46-3.739.30.23613200.9570.0790.251.30796.5
3.73-4.1110.80.2213380.9590.0670.231.23197.5
4.11-4.713.70.17113760.990.0460.1771.09199.6
4.7-5.9214.50.11913820.9960.0310.1231.052100
5.92-4014.50.06914300.9980.0190.0711.05998.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U9U Fab heavy chain, and 2XQY Fab light chain

3u9u

2xqy


Resolution: 2.75→26.41 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.88 / SU B: 19.049 / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2699 648 5.2 %RANDOM
Rwork0.2307 ---
obs0.2328 11735 93.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.09 Å2 / Biso mean: 40.324 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.17 Å20 Å2-0.83 Å2
2--3.29 Å20 Å2
3---0.52 Å2
Refinement stepCycle: final / Resolution: 2.75→26.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3355 0 0 26 3381
Biso mean---25.32 -
Num. residues----455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0133443
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173030
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.6424712
X-RAY DIFFRACTIONr_angle_other_deg1.0921.5687050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4455452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62122.937126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88615504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4151510
X-RAY DIFFRACTIONr_chiral_restr0.0390.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023861
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02685
LS refinement shellResolution: 2.75→2.821 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 35 -
Rwork0.337 868 -
all-903 -
obs--93 %

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