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- PDB-5vco: THE CRYSTAL STRUCTURE OF DER P 1 ALLERGEN COMPLEXED WITH FAB FRAG... -

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Basic information

Entry
Database: PDB / ID: 5vco
TitleTHE CRYSTAL STRUCTURE OF DER P 1 ALLERGEN COMPLEXED WITH FAB FRAGMENT OF MAB 10B9
Components
  • HEAVY CHAIN OF FAB FRAGMENT OF 10B9 ANTIBODY
  • LIGHT CHAIN OF FAB FRAGMENT OF 10B9 ANTIBODY
  • PEPTIDASE 1Protease
KeywordsIMMUNE SYSTEM / ALLERGEN / ANTIBODY
Function / homology
Function and homology information


peptidase 1 (mite) / cysteine-type peptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Peptidase 1 / Der p 1 allergen
Similarity search - Component
Biological speciesMus musculus (house mouse)
Dermatophagoides pteronyssinus (European house dust mite)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsOsinski, T. / Majorek, K.A. / Pomes, A. / Offermann, L.R. / Osinski, S. / Glesner, J. / Vailes, L.D. / Chapman, M.D. / Minor, W. / Chruszcz, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI077653 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM53163 United States
CitationJournal: J. Immunol. / Year: 2015
Title: Structural Analysis of Der p 1-Antibody Complexes and Comparison with Complexes of Proteins or Peptides with Monoclonal Antibodies.
Authors: Osinski, T. / Pomes, A. / Majorek, K.A. / Glesner, J. / Offermann, L.R. / Vailes, L.D. / Chapman, M.D. / Minor, W. / Chruszcz, M.
History
DepositionMar 31, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionApr 26, 2017ID: 4PP2
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Apr 13, 2022Group: Database references / Structure summary
Category: audit_author / chem_comp ...audit_author / chem_comp / citation_author / database_2
Item: _audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms ..._audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 27, 2022Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
Revision 1.6Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIGHT CHAIN OF FAB FRAGMENT OF 10B9 ANTIBODY
B: HEAVY CHAIN OF FAB FRAGMENT OF 10B9 ANTIBODY
C: LIGHT CHAIN OF FAB FRAGMENT OF 10B9 ANTIBODY
D: HEAVY CHAIN OF FAB FRAGMENT OF 10B9 ANTIBODY
E: PEPTIDASE 1
F: PEPTIDASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,38310
Polymers144,8616
Non-polymers5234
Water39622
1
A: LIGHT CHAIN OF FAB FRAGMENT OF 10B9 ANTIBODY
B: HEAVY CHAIN OF FAB FRAGMENT OF 10B9 ANTIBODY
F: PEPTIDASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6925
Polymers72,4303
Non-polymers2612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: LIGHT CHAIN OF FAB FRAGMENT OF 10B9 ANTIBODY
D: HEAVY CHAIN OF FAB FRAGMENT OF 10B9 ANTIBODY
E: PEPTIDASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6925
Polymers72,4303
Non-polymers2612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.685, 74.852, 184.103
Angle α, β, γ (deg.)90.00, 97.42, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13E
23F

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPARGARGAA1 - 2111 - 211
21ASPASPARGARGCC1 - 2111 - 211
12GLUGLUARGARGBB1 - 2221 - 222
22GLUGLUARGARGDD1 - 2221 - 222
13THRTHRLEULEUEE1 - 2221 - 222
23THRTHRLEULEUFF1 - 2221 - 222

NCS ensembles :
ID
2
1
3

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Components

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody LIGHT CHAIN OF FAB FRAGMENT OF 10B9 ANTIBODY


Mass: 23280.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HYBRIDOMA / Production host: MUS MUSCULUS (house mouse)
#2: Antibody HEAVY CHAIN OF FAB FRAGMENT OF 10B9 ANTIBODY


Mass: 24135.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HYBRIDOMA / Production host: MUS MUSCULUS (house mouse)

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Protein / Sugars , 2 types, 4 molecules EF

#3: Protein PEPTIDASE 1 / Protease / ALLERGEN DER P I / MAJOR MITE FECAL ALLERGEN DER P 1


Mass: 25014.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Dermatophagoides pteronyssinus (European house dust mite)
References: UniProt: Q3HWZ5, UniProt: P08176*PLUS
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 24 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.39 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100 MM NA ACETATE, 8% W/V PEG 4000, 15% MPD, PH 4.5
PH range: 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.51201 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2011 / Details: BERYLLIUM LENSES
RadiationMonochromator: DIAMOND 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.51201 Å / Relative weight: 1
ReflectionResolution: 2.74→50 Å / Num. obs: 36141 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 55.2 Å2 / Rmerge(I) obs: 0.139 / Rsym value: 0.139 / Net I/σ(I): 14.5
Reflection shellResolution: 2.74→2.79 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.684 / % possible all: 97.9

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
REFMAC5.7.0029refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F5V, 3RVT

3f5v

3rvt


Resolution: 2.74→47.26 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.89 / SU B: 33.171 / SU ML: 0.301 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.393 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1786 5 %RANDOM
Rwork0.2 ---
obs0.203 34176 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.94 Å2
Baniso -1Baniso -2Baniso -3
1-7.5 Å2-0 Å2-4.07 Å2
2---5.09 Å2-0 Å2
3----1.82 Å2
Refinement stepCycle: LAST / Resolution: 2.74→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9866 0 30 22 9918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0210151
X-RAY DIFFRACTIONr_bond_other_d0.0010.028992
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.93813892
X-RAY DIFFRACTIONr_angle_other_deg0.7153.00320579
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.23951292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46324.07430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.713151455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9181546
X-RAY DIFFRACTIONr_chiral_restr0.0670.21566
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02111762
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022392
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A11990.09
12C11990.09
21B11680.06
22D11680.06
31E13120.09
32F13120.09
LS refinement shellResolution: 2.74→2.81 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 118 -
Rwork0.32 2482 -
obs--97.6 %
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)
10.6547-0.08530.0720.78110.4121.0472-0.0144-0.03120.0282-0.07390.0252-0.0237-0.00270.0256-0.01080.10510.01040.00220.1430.02110.12715.643-19.421109.338
21.50020.4143-0.74970.4195-0.05790.74710.03970.02530.10670.0383-0.0050.04330.00330.024-0.03460.0470.0116-0.00020.1476-0.01720.1821-16.193-14.959138.871
30.63770.3997-0.16140.7193-0.37221.0303-0.024-0.0174-0.02160.0004-0.0182-0.00920.0239-0.03920.04230.12540.0065-0.04150.1182-0.00530.1275-14.683-22.83497.863
41.95460.7754-0.62230.5028-0.35480.42490.0236-0.00250.0015-0.02620.04470.0258-0.0384-0.0508-0.06830.1198-0.0009-0.01760.14630.00860.1274-9.665-21.579101.231
50.5306-0.19990.35751.18130.97321.4152-0.0310.00390.0894-0.03460.0118-0.0347-0.0587-0.0840.01930.04540.0113-0.00730.17170.04810.1993-24.157-10.277125.309
60.27010.1993-0.15790.7665-0.63951.4362-0.0048-0.02610.0481-0.0082-0.01280.05230.0385-0.00370.01760.00910.0130.03540.2055-0.02290.19375.0771.76818.976
71.46320.31511.02960.41520.31241.1732-0.0284-0.01530.01790.06960.0030.0123-0.0476-0.05050.02530.0384-0.00590.0390.16750.02130.153221.08-1.48451.783
80.30160.26130.47651.07630.68681.1887-0.01520.0689-0.00840.00960.0014-0.0337-0.04840.07530.01370.01820.00520.04970.20350.01880.209527.1674.84210.75
91.11030.49980.80640.87470.35350.7039-0.0090.0383-0.0189-0.04390.0346-0.0766-0.0402-0.005-0.02560.02080.0110.04770.21670.0120.196321.7063.65713.421
100.60730.3884-0.00391.2259-0.17720.51580.0277-0.0056-0.02040.0263-0.03540.03180.01410.00610.00770.01430.00220.04680.20640.00140.1831.184-7.61340.645
110.4924-0.25060.06550.4809-0.09240.34460.01210.02170.0152-0.0303-0.01030.01010.04820.0073-0.00180.0211-0.00510.04480.1896-0.0090.16980.5976.208-15.218
120.4356-0.0069-0.1030.4810.14240.1046-0.01260.0201-0.0704-0.0428-0.01420.0283-0.07550.0190.02670.1829-0.0137-0.03050.11870.00810.094515.039-23.7476.139
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 105
2X-RAY DIFFRACTION2A106 - 211
3X-RAY DIFFRACTION3B1 - 80
4X-RAY DIFFRACTION4B81 - 120
5X-RAY DIFFRACTION5B121 - 222
6X-RAY DIFFRACTION6C1 - 105
7X-RAY DIFFRACTION7C106 - 211
8X-RAY DIFFRACTION8D1 - 80
9X-RAY DIFFRACTION9D81 - 120
10X-RAY DIFFRACTION10D121 - 222
11X-RAY DIFFRACTION11E1 - 222
12X-RAY DIFFRACTION12F1 - 222

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