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- PDB-5vpl: CRYSTAL STRUCTURE OF DER F 1 COMPLEXED WITH FAB 4C1 -

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Basic information

Entry
Database: PDB / ID: 5vpl
TitleCRYSTAL STRUCTURE OF DER F 1 COMPLEXED WITH FAB 4C1
Components
  • 4C1 - HEAVY CHAIN
  • 4C1 - LIGHT CHAIN
  • Der f 1 variant
KeywordsHYDROLASE/IMMUNE SYSTEM / COMPLEX BETWEEN AN ALLERGEN AND FAB FRAGMENT OF 4C1 ANTIBODY / HYDROLASE-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


peptidase 1 (mite) / immunoglobulin complex / cysteine-type peptidase activity / adaptive immune response / proteolysis / extracellular region / plasma membrane
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / 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 ...Cathepsin propeptide inhibitor domain (I29) / 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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 / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Der f 1 variant / Peptidase 1 / Anti-colorectal carcinoma light chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Dermatophagoides farinae (American house dust mite)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChruszcz, M. / Vailes, L.D. / Chapman, M.D. / Pomes, A. / Minor, W.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Molecular Determinants For Antibody Binding On Group 1 House Dust Mite Allergens.
Authors: Chruszcz, M. / Pomes, A. / Glesner, J. / Vailes, L.D. / Osinski, T. / Porebski, P.J. / Majorek, K.A. / Heymann, P.W. / Platts-Mills, T.A. / Minor, W. / Chapman, M.D.
History
DepositionMay 5, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionMay 24, 2017ID: 3RVV
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 1.2Apr 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 1.3Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_conn_type
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 / _pdbx_nonpoly_scheme.auth_seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Der f 1 variant
C: 4C1 - LIGHT CHAIN
D: 4C1 - HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2959
Polymers76,7863
Non-polymers5106
Water11,710650
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-16 kcal/mol
Surface area28340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.403, 79.428, 72.199
Angle α, β, γ (deg.)90.00, 105.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 2 molecules CD

#2: Antibody 4C1 - LIGHT CHAIN


Mass: 23937.645 Da / Num. of mol.: 1
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) / References: UniProt: Q7TS98
#3: Antibody 4C1 - HEAVY CHAIN


Mass: 27677.270 Da / Num. of mol.: 1
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, 2 molecules A

#1: Protein Der f 1 variant


Mass: 25170.975 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 99-321 / Source method: isolated from a natural source
Source: (natural) Dermatophagoides farinae (American house dust mite)
References: UniProt: I2CMD3, UniProt: P16311*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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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 , 3 types, 655 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 650 / 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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.1M HEPES, 18% W/V PEG12K, 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: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2008 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 55979 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 23.6
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.557 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
REFMAC5.8.0158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3D6S, 1MLB

3d6s
PDB Unreleased entry

1mlb


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.952 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.125 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19421 2783 5 %RANDOM
Rwork0.15169 ---
obs0.15376 53171 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å2-0.05 Å2
2--1.02 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5093 0 31 650 5774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.025337
X-RAY DIFFRACTIONr_bond_other_d00.024676
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.9427276
X-RAY DIFFRACTIONr_angle_other_deg3.798310900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4875664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96423.872235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.31415840
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8971530
X-RAY DIFFRACTIONr_chiral_restr0.1120.2799
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0215959
X-RAY DIFFRACTIONr_gen_planes_other0.0260.021107
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_it1.1692.0052641
X-RAY DIFFRACTIONr_mcbond_other1.1682.0032640
X-RAY DIFFRACTIONr_mcangle_it1.8212.9973310
X-RAY DIFFRACTIONr_mcangle_other1.8222.9983311
X-RAY DIFFRACTIONr_scbond_it1.8682.262696
X-RAY DIFFRACTIONr_scbond_other1.8672.2582694
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.993.2983966
X-RAY DIFFRACTIONr_long_range_B_refined5.82424.856076
X-RAY DIFFRACTIONr_long_range_B_other5.71424.4836016
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 189 -
Rwork0.235 3809 -
obs--97.58 %
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)
10.8617-0.05280.09981.23060.36540.91450.0290.04150.0634-0.0331-0.03160.1297-0.0334-0.07960.00260.0109-0.0068-0.02170.0645-0.00790.128934.83812.83329.79
20.9068-0.27780.24010.5956-0.01791.06180.0185-0.1272-0.0748-0.02140.00920.04220.12340.0079-0.02760.0327-0.0046-0.00870.05890.00280.116643.0274.18134.436
31.1695-0.8463-0.32841.15860.16550.99880.0268-0.0408-0.015-0.0452-0.03640.03290.03650.07620.00960.02880.0072-0.01240.0631-0.01340.123976.762-0.64920.055
41.13090.3094-1.28592.1055-2.48275.54210.0372-0.15250.0146-0.0120.0408-0.1972-0.090.7043-0.07790.0042-0.03020.01320.2418-0.08740.1185100.9542.017-7.836
50.97040.244-0.65730.7125-0.27661.33030.03660.07190.0703-0.09360.01320.0128-0.1139-0.1447-0.04980.05060.0327-0.01180.0559-0.00260.118464.49312.427.996
61.3778-1.1921-0.65232.84391.27841.59960.08410.1210.0233-0.14390.0287-0.1245-0.0354-0.0012-0.11280.05370.0110.00380.0699-0.00690.065785.8980.656-13.403
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 104
2X-RAY DIFFRACTION2A105 - 223
3X-RAY DIFFRACTION3C1 - 107
4X-RAY DIFFRACTION4C108 - 211
5X-RAY DIFFRACTION5D1 - 121
6X-RAY DIFFRACTION6D122 - 222

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