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- PDB-3so3: Structures of Fab-Protease Complexes Reveal a Highly Specific Non... -

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Basic information

Entry
Database: PDB / ID: 3so3
TitleStructures of Fab-Protease Complexes Reveal a Highly Specific Non-Canonical Mechanism of Inhibition.
Components
  • A11 FAB heavy chain
  • A11 FAB light chain
  • Suppressor of tumorigenicity 14 protein
KeywordsHYDROLASE / antibody-protein / protein-protein / protease inhibitor / disease mutation / glycoprotein / membrane / serine protease / signal-anchor / transmembrane
Function / homology
Function and homology information


matriptase / epithelial cell morphogenesis involved in placental branching / acrosome reaction / Formation of the cornified envelope / keratinocyte differentiation / serine-type peptidase activity / neural tube closure / protein catabolic process / basolateral plasma membrane / external side of plasma membrane ...matriptase / epithelial cell morphogenesis involved in placental branching / acrosome reaction / Formation of the cornified envelope / keratinocyte differentiation / serine-type peptidase activity / neural tube closure / protein catabolic process / basolateral plasma membrane / external side of plasma membrane / serine-type endopeptidase activity / proteolysis / extracellular space / plasma membrane
Similarity search - Function
Peptidase S1A, matripase / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily ...Peptidase S1A, matripase / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
sucrose / Suppressor of tumorigenicity 14 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSchneider, E.L. / Farady, C.J. / Egea, P.F. / Goetz, D.H. / Baharuddin, A. / Craik, C.S.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: A reverse binding motif that contributes to specific protease inhibition by antibodies.
Authors: Schneider, E.L. / Lee, M.S. / Baharuddin, A. / Goetz, D.H. / Farady, C.J. / Ward, M. / Wang, C.I. / Craik, C.S.
History
DepositionJun 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_alt_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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Suppressor of tumorigenicity 14 protein
B: A11 FAB light chain
C: A11 FAB heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3315
Polymers73,8973
Non-polymers4342
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-35 kcal/mol
Surface area27400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.598, 130.598, 96.941
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

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Antibody , 2 types, 2 molecules BC

#2: Antibody A11 FAB light chain


Mass: 23627.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#3: Antibody A11 FAB heavy chain


Mass: 23821.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Suppressor of tumorigenicity 14 protein / Matriptase / Membrane-type serine protease 1 / MT-SP1 / Prostamin / Serine protease 14 / Serine ...Matriptase / Membrane-type serine protease 1 / MT-SP1 / Prostamin / Serine protease 14 / Serine protease TADG-15 / Tumor-associated differentially-expressed gene 15 protein


Mass: 26447.689 Da / Num. of mol.: 1 / Fragment: PEPTIDASE S1 DOMAIN / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS14, SNC19, ST14, TADG15 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1BLUE / References: UniProt: Q9Y5Y6, matriptase
#4: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 2 types, 462 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 3.23 Å3/Da / Density % sol: 61.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 16% PEG 3350, 0.23 M MgSO4, 0.4% isopropanol, 3% glycerol, 0.12 M AMSO4, vapor diffusion, hanging drop, temperature 293k, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 8, 2007 / Details: KOHZU: DOUBLE CRYSTAL SI(111)
RadiationMonochromator: KOHZU: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.54181
ReflectionResolution: 2.1→113 Å / Num. all: 56788 / Num. obs: 54872 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 54.04 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.094 / Net I/σ(I): 11.7
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.863 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.932 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
StructureStudiodata collection
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EAX

1eax


Resolution: 2.1→19.88 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 7.365 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.194 2774 5.1 %RANDOM
Rwork0.161 ---
obs0.162 51934 99.7 %-
all-56788 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 61.253 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å2-0.27 Å20 Å2
2---0.53 Å20 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5106 0 29 461 5596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225276
X-RAY DIFFRACTIONr_bond_other_d0.0020.023530
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.9527189
X-RAY DIFFRACTIONr_angle_other_deg0.9183.0038581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6495673
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43223.632212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6715794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4381529
X-RAY DIFFRACTIONr_chiral_restr0.0980.2798
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025913
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021077
X-RAY DIFFRACTIONr_nbd_refined0.190.2941
X-RAY DIFFRACTIONr_nbd_other0.2020.23735
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22526
X-RAY DIFFRACTIONr_nbtor_other0.090.22850
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2416
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2130.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2410.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.081.54238
X-RAY DIFFRACTIONr_mcbond_other0.2091.51379
X-RAY DIFFRACTIONr_mcangle_it1.30325389
X-RAY DIFFRACTIONr_scbond_it2.25932288
X-RAY DIFFRACTIONr_scangle_it3.1744.51799
X-RAY DIFFRACTIONr_rigid_bond_restr2.37835275
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 205 -
Rwork0.216 3815 -
obs--99.55 %
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)
13.93450.10551.84961.32690.27442.58560.08550.1717-0.33140.16880.0039-0.16880.27610.175-0.0894-0.12430.0232-0.1344-0.195-0.0611-0.1561116.88522.4575.628
22.2518-0.48950.97070.9675-0.3321.7411-0.10520.14990.08630.05460.0033-0.1256-0.10270.03560.102-0.1746-0.0545-0.0774-0.1582-0.0488-0.225889.16435.69-9.697
34.1148-0.7233-2.97860.89570.63015.34940.20510.02540.6716-0.25090.0475-0.0375-1.0635-0.0498-0.25260.2011-0.059-0.047-0.06740.0105-0.141964.6154.113-24.902
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 244
2X-RAY DIFFRACTION2B1 - 110
3X-RAY DIFFRACTION2C1 - 125
4X-RAY DIFFRACTION3B111 - 213
5X-RAY DIFFRACTION3C126 - 213

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