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

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Basic information

Entry
Database: PDB / ID: 5vcn
TitleTHE CRYSTAL STRUCTURE OF DER P 1 ALLERGEN COMPLEXED WITH FAB FRAGMENT OF MAB 5H8
Components
  • HEAVY CHAIN OF FAB FRAGMENT OF MAB 5H8
  • LIGHT CHAIN OF FAB FRAGMENT OF MAB 5H8
  • PEPTIDASE 1
KeywordsIMMUNE SYSTEM / ALLERGEN / ANTIBODY
Function / homology
Function and homology information


peptidase 1 (mite) / proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space / 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
PHOSPHATE ION / 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: 3 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: 4PP1
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Derived calculations
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / 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 1.5Apr 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 1.6Apr 27, 2022Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_wavelength_list
Revision 1.7Oct 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: PEPTIDASE 1
B: PEPTIDASE 1
C: LIGHT CHAIN OF FAB FRAGMENT OF MAB 5H8
D: HEAVY CHAIN OF FAB FRAGMENT OF MAB 5H8
E: LIGHT CHAIN OF FAB FRAGMENT OF MAB 5H8
F: HEAVY CHAIN OF FAB FRAGMENT OF MAB 5H8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,33314
Polymers152,4966
Non-polymers8378
Water1,33374
1
A: PEPTIDASE 1
E: LIGHT CHAIN OF FAB FRAGMENT OF MAB 5H8
F: HEAVY CHAIN OF FAB FRAGMENT OF MAB 5H8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6677
Polymers76,2483
Non-polymers4184
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PEPTIDASE 1
C: LIGHT CHAIN OF FAB FRAGMENT OF MAB 5H8
D: HEAVY CHAIN OF FAB FRAGMENT OF MAB 5H8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6677
Polymers76,2483
Non-polymers4184
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.743, 73.263, 200.340
Angle α, β, γ (deg.)90.00, 91.09, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22E
13D
23F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLEULEUAA1 - 2221 - 222
21THRTHRLEULEUBB1 - 2221 - 222
12ASPASPARGARGCC1 - 2101 - 210
22ASPASPARGARGEE1 - 2101 - 210
13GLUGLUARGARGDD1 - 2201 - 220
23GLUGLUARGARGFF1 - 2201 - 220

NCS ensembles :
ID
1
2
3

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Components

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Antibody , 2 types, 4 molecules CEDF

#2: Antibody LIGHT CHAIN OF FAB FRAGMENT OF MAB 5H8


Mass: 23232.600 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)
#3: Antibody HEAVY CHAIN OF FAB FRAGMENT OF MAB 5H8


Mass: 28000.816 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 AB

#1: Protein PEPTIDASE 1 / 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
#7: 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


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 , 4 types, 80 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.3 Å3/Da / Density % sol: 46.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 MM MES, 10% W/V PEG 6000, 5% MPD, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2011 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 28001 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.165 / Rsym value: 0.165 / Net I/σ(I): 10
Reflection shellResolution: 3→3.05 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.653 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
REFMAC5.8.0049refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F5V, 3RVT

3f5v

3rvt


Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.857 / SU B: 50.017 / SU ML: 0.432 / Cross valid method: THROUGHOUT / ESU R Free: 0.492 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1404 5 %RANDOM
Rwork0.219 ---
obs0.221 26581 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.05 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å2-0 Å2-1.27 Å2
2---3.39 Å2-0 Å2
3---2.21 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9748 0 48 74 9870
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0210036
X-RAY DIFFRACTIONr_bond_other_d0.0030.028868
X-RAY DIFFRACTIONr_angle_refined_deg1.2471.94113728
X-RAY DIFFRACTIONr_angle_other_deg1.364320312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.67651283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04224.178426
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.636151434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9221547
X-RAY DIFFRACTIONr_chiral_restr0.0630.21543
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111656
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022353
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_it1.5471.5195156
X-RAY DIFFRACTIONr_mcbond_other1.5471.5195155
X-RAY DIFFRACTIONr_mcangle_it2.6962.276431
X-RAY DIFFRACTIONr_mcangle_other1.9131.5996432
X-RAY DIFFRACTIONr_scbond_it1.7041.6064880
X-RAY DIFFRACTIONr_scbond_other1.3971.1394880
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1541.687298
X-RAY DIFFRACTIONr_long_range_B_refined4.268.36711254
X-RAY DIFFRACTIONr_long_range_B_other4.268.37311255
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)
11A124250.08
12B124250.08
21C108920.07
22E108920.07
31D111060.09
32F111060.09
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 115 -
Rwork0.304 1913 -
obs--100 %
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)
12.88641.2314-0.67230.7863-1.05382.45150.02340.02530.06090.1019-0.04220.0134-0.24920.3180.01880.33410.01320.0350.3788-0.00270.339414.82983.273726.4705
21.1998-0.04030.42550.4006-0.55050.88090.13830.01360.01160.03620.00010.0599-0.02090.0093-0.13830.40410.00130.05620.40930.010.3879-0.5567-0.852320.471
30.1720.40190.01991.04410.58613.67490.1687-0.0891-0.04210.3438-0.2626-0.1187-00.18090.09390.52810.0249-0.0220.44060.02460.18946.76841.077238.0452
40.26940.6334-0.32842.6868-1.67711.1532-0.15850.06810.14590.36890.03270.0514-0.2532-0.1030.12580.6706-0.03610.01890.3088-0.00770.40997.5086-1.509339.4156
50.5923-0.15180.47121.74620.81680.89510.0176-0.0862-0.0159-0.0247-0.06490.1524-0.0044-0.0710.04730.450.0280.04840.43390.02610.30867.05220.569634.2861
60.60780.0569-0.4490.0145-0.03721.3937-0.09740.0085-0.03190.0373-0.05240.02550.01370.03490.14990.4688-0.0091-0.02710.3449-0.04140.438515.179627.2126.985
72.57270.7648-0.32351.26670.89691.00990.0109-0.02920.0526-0.00740.0202-0.01770.07890.0325-0.03110.41260.0397-0.06730.4150.03150.328924.605729.3978118.4072
80.5147-0.03640.13030.7485-0.31710.5252-0.17430.05650.08060.14870.14450.07270.1255-0.03310.02980.38720.0565-0.02820.3942-0.03040.373418.069732.7141125.5804
92.08872.6213-2.11173.2961-2.6582.1559-0.0323-0.23810.0222-0.1725-0.11370.01440.18170.16710.14590.75020.1194-0.07180.5132-0.08460.093819.364527.5942145.963
101.9676-0.93520.54081.744-0.80030.4977-0.0193-0.05610.13690.1256-0.01460.11040.09810.16250.03390.50890.0611-0.02240.3595-0.02270.309415.166629.1844135.7994
113.5768-0.8104-0.84773.2762-1.79341.4897-0.03780.09310.16010.710.56610.6926-0.5238-0.3915-0.52840.58670.0789-0.05780.27730.03980.45081.223239.300191.321
120.51990.37650.55280.29480.32111.0128-0.09820.01590.1034-0.05020.04850.0561-0.08450.02810.04970.44830.0085-0.08990.38330.01690.39923.895134.074286.1921
130.97191.28310.583.49020.45750.5924-0.0914-0.20940.0351-0.0233-0.06550.09040.0181-0.16360.15690.46140.0485-0.09910.3960.06110.3128-15.917326.612268.1811
140.01520.10610.09641.47241.34671.2652-0.02970.04770.02540.07340.02580.05360.1830.08670.0040.47730.0274-0.06280.3998-0.02410.349615.165216.858693.8019
151.48450.14141.32150.15880.16621.19340.00450.0241-0.03920.0090.04070.0360.05470.0631-0.04510.5031-0.012-0.01470.3933-0.01980.316912.607816.091190.2783
160.7905-0.24730.83081.3206-0.93371.7945-0.15350.0208-0.064-0.08110.2563-0.2688-0.057-0.1878-0.10280.4714-0.0491-0.05380.37410.02830.3327-0.951521.364960.1598
170.24830.58090.24662.34451.52765.4103-0.23660.02970.0019-0.05240.2568-0.01540.17260.6815-0.02020.37060.03990.03230.37760.05220.382520.6943-9.4052-9.4246
180.36460.3165-0.57050.56-0.33261.0329-0.1054-0.0193-0.1134-0.0920.0232-0.05610.10640.02640.08220.43510.00870.05860.39780.00330.369120.9591-3.4864-17.3698
191.3730.79070.37160.54740.30290.2033-0.2422-0.0269-0.2611-0.14090.1589-0.092-0.0460.09750.08340.5030.06170.18960.3475-0.06010.413339.18294.0178-35.7396
200.0177-0.10440.09391.1292-1.04190.99170.00540.0429-0.03980.05590.00940.0101-0.1618-0.02-0.01480.40380.03370.02560.45250.00120.41156.592612.5697-6.5323
210.47070.0409-0.52820.1708-0.04250.6149-0.01570.0116-0.0215-0.05720.027-0.04420.0432-0.1004-0.01140.4410.00130.01510.4350.02560.349913.310311.4267-19.9416
221.581-1.4019-1.60551.25221.41222.52410.05080.0859-0.0192-0.1206-0.06510.003-0.1163-0.05720.01430.5498-0.06780.07660.3805-0.02640.2622.0339.1381-41.4405
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 25
2X-RAY DIFFRACTION2A26 - 130
3X-RAY DIFFRACTION3A131 - 161
4X-RAY DIFFRACTION4A162 - 185
5X-RAY DIFFRACTION5A186 - 222
6X-RAY DIFFRACTION6B1 - 43
7X-RAY DIFFRACTION7B44 - 96
8X-RAY DIFFRACTION8B97 - 149
9X-RAY DIFFRACTION9B150 - 166
10X-RAY DIFFRACTION10B167 - 222
11X-RAY DIFFRACTION11C1 - 19
12X-RAY DIFFRACTION12C20 - 138
13X-RAY DIFFRACTION13C139 - 210
14X-RAY DIFFRACTION14D1 - 62
15X-RAY DIFFRACTION15D63 - 129
16X-RAY DIFFRACTION16D130 - 220
17X-RAY DIFFRACTION17E1 - 18
18X-RAY DIFFRACTION18E19 - 169
19X-RAY DIFFRACTION19E170 - 210
20X-RAY DIFFRACTION20F1 - 62
21X-RAY DIFFRACTION21F63 - 171
22X-RAY DIFFRACTION22F172 - 220

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