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- PDB-5vyf: Structure of single chain Fel d 1 bound to a neutralizing antibody -

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Basic information

Entry
Database: PDB / ID: 5vyf
TitleStructure of single chain Fel d 1 bound to a neutralizing antibody
Components
  • Antibody Fab heavy chain
  • Antibody light chainImmunoglobulin light chain
  • Chimera of Major allergen I polypeptide chain 2,Major allergen I polypeptide chain 1
KeywordsIMMUNE SYSTEM / antibody / allergen / therapeutic
Function / homology
Function and homology information


steroid binding / extracellular space / extracellular region
Similarity search - Function
Histone Acetyltransferase; Chain A - #50 / Major allergen I polypeptide chain 1 / Major allergen I polypeptide chain 2-like / Allergen Fel d I-B chain / Uteroglobin / Secretoglobin / Uteroglobin family / Secretoglobin (SCGB) family profile. / Secretoglobin superfamily / Histone Acetyltransferase; Chain A ...Histone Acetyltransferase; Chain A - #50 / Major allergen I polypeptide chain 1 / Major allergen I polypeptide chain 2-like / Allergen Fel d I-B chain / Uteroglobin / Secretoglobin / Uteroglobin family / Secretoglobin (SCGB) family profile. / Secretoglobin superfamily / Histone Acetyltransferase; Chain A / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Major allergen I polypeptide chain 1 / Major allergen I polypeptide chain 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Felis catus (domestic cat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsFranklin, M.C.
CitationJournal: Nat Commun / Year: 2018
Title: Treating cat allergy with monoclonal IgG antibodies that bind allergen and prevent IgE engagement.
Authors: Orengo, J.M. / Radin, A.R. / Kamat, V. / Badithe, A. / Ben, L.H. / Bennett, B.L. / Zhong, S. / Birchard, D. / Limnander, A. / Rafique, A. / Bautista, J. / Kostic, A. / Newell, D. / Duan, X. ...Authors: Orengo, J.M. / Radin, A.R. / Kamat, V. / Badithe, A. / Ben, L.H. / Bennett, B.L. / Zhong, S. / Birchard, D. / Limnander, A. / Rafique, A. / Bautista, J. / Kostic, A. / Newell, D. / Duan, X. / Franklin, M.C. / Olson, W. / Huang, T. / Gandhi, N.A. / Lipsich, L. / Stahl, N. / Papadopoulos, N.J. / Murphy, A.J. / Yancopoulos, G.D.
History
DepositionMay 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Antibody light chain
H: Antibody Fab heavy chain
F: Chimera of Major allergen I polypeptide chain 2,Major allergen I polypeptide chain 1
A: Antibody light chain
B: Antibody Fab heavy chain
C: Chimera of Major allergen I polypeptide chain 2,Major allergen I polypeptide chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,6668
Polymers137,5866
Non-polymers802
Water1,820101
1
L: Antibody light chain
H: Antibody Fab heavy chain
F: Chimera of Major allergen I polypeptide chain 2,Major allergen I polypeptide chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8334
Polymers68,7933
Non-polymers401
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-43 kcal/mol
Surface area25000 Å2
MethodPISA
2
A: Antibody light chain
B: Antibody Fab heavy chain
C: Chimera of Major allergen I polypeptide chain 2,Major allergen I polypeptide chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8334
Polymers68,7933
Non-polymers401
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-43 kcal/mol
Surface area24660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.985, 131.480, 148.357
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21A
12H
22B
13F
23C

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
11ASPASPASNASNLA1 - 2101 - 210
21ASPASPASNASNAD1 - 2101 - 210
12VALVALVALVALHB2 - 2132 - 213
22VALVALVALVALBE2 - 2132 - 213
13CYSCYSLEULEUFC7 - 1617 - 161
23CYSCYSLEULEUCF7 - 1617 - 161

NCS ensembles :
ID
3
1
2

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Components

#1: Antibody Antibody light chain / Immunoglobulin light chain


Mass: 23400.018 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody Antibody Fab heavy chain


Mass: 23473.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein Chimera of Major allergen I polypeptide chain 2,Major allergen I polypeptide chain 1 / AG4 / Allergen Cat-1 / Allergen Fel d I-B / Allergen FdI / AG4 / Allergen Cat-1 / Allergen Fel d I- ...AG4 / Allergen Cat-1 / Allergen Fel d I-B / Allergen FdI / AG4 / Allergen Cat-1 / Allergen Fel d I-A / Allergen Fel dI


Mass: 21919.871 Da / Num. of mol.: 2 / Fragment: UNP P30440 residues 18-109, UNP P30438 23-92 / Mutation: N50A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Felis catus (domestic cat) / Gene: CH2, CH1 / Production host: Homo sapiens (human) / References: UniProt: P30440, UniProt: P30438
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.83 Å3/Da / Density % sol: 56.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: calcium acetate, sodium cacodylate, PEG 300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→98.4 Å / Num. obs: 33144 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.055 / Χ2: 0.853 / Net I/σ(I): 14.9
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1596 / CC1/2: 0.753 / Rpim(I) all: 0.446 / Χ2: 0.59 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PUO, 2R8S

1puo

2r8s


Resolution: 2.9→98.4 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.89 / SU B: 39.219 / SU ML: 0.332 / Cross valid method: THROUGHOUT / ESU R Free: 0.406 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25942 1643 5.1 %RANDOM
Rwork0.22538 ---
obs0.22711 30883 98.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 59.128 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.54 Å20 Å2
3---0.72 Å2
Refinement stepCycle: 1 / Resolution: 2.9→98.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8460 0 2 101 8563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.028642
X-RAY DIFFRACTIONr_bond_other_d0.0020.028066
X-RAY DIFFRACTIONr_angle_refined_deg1.1741.96211736
X-RAY DIFFRACTIONr_angle_other_deg0.962318662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15551098
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47224.556338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.367151436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.571536
X-RAY DIFFRACTIONr_chiral_restr0.0740.21354
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219672
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021868
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_it0.5583.4374422
X-RAY DIFFRACTIONr_mcbond_other0.5583.4364421
X-RAY DIFFRACTIONr_mcangle_it1.0065.155510
X-RAY DIFFRACTIONr_mcangle_other1.0065.1515511
X-RAY DIFFRACTIONr_scbond_it0.533.484220
X-RAY DIFFRACTIONr_scbond_other0.533.484220
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9475.1996227
X-RAY DIFFRACTIONr_long_range_B_refined2.86526.6618940
X-RAY DIFFRACTIONr_long_range_B_other2.86126.6578936
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)
11L239780.01
12A239780.01
21H224920.03
22B224920.03
31F167780
32C167780
LS refinement shellResolution: 2.903→2.978 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 110 -
Rwork0.303 1919 -
obs--84.93 %
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)
12.6067-1.2342-0.33665.04580.59381.4074-0.0887-0.1618-0.16510.39410.13260.1180.2793-0.0589-0.04390.15840.0696-0.01660.0818-0.00120.0451-12.1019-1.190147.1377
21.6296-0.85241.40962.3594-1.35198.8630.03730.1240.0857-0.258-0.0264-0.42710.06390.3273-0.0110.1260.03530.01510.09-0.12250.2771-11.0433-17.048614.8621
31.49860.01630.6362.76181.89594.1886-0.0705-0.0843-0.10160.19390.07690.32280.15330.051-0.00630.02460.00310.02890.0173-0.00640.1371-28.958110.961536.8559
44.96-2.34990.19666.1719-0.31262.33530.02980.0021-0.62130.19780.14670.23350.56040.0012-0.17650.2106-0.0001-0.05650.0831-0.06150.1385-27.2781-18.341818.3741
53.17550.36590.21785.1981-0.89943.249-0.1194-0.3017-0.0910.55890.0771-0.293-0.03830.25650.04230.17130.0990.01750.150.00370.0577-18.779631.975661.2608
63.1116-1.2899-0.63584.0292-0.45361.2087-0.1252-0.34520.43770.26670.0982-0.11870.01740.08790.0270.16460.1288-0.08080.1339-0.10650.11629.8015-3.748247.317
72.0139-0.9612-3.48122.4221.37479.6540.24271.09350.5085-0.4307-0.06030.19110.106-1.3146-0.18250.27590.1715-0.05890.88730.4080.60478.58612.96215.7389
81.79420.4717-0.73293.2279-1.51023.1049-0.1931-0.18520.14980.17220.1266-0.3751-0.10850.14530.06650.08460.0476-0.09570.0488-0.07210.186627.0223-15.113437.0301
96.4693-3.6292-0.72233.3443-0.34443.30250.27750.46191.5777-0.16520.2039-0.3891-0.6234-0.3138-0.48140.30430.02750.07920.3440.19560.76624.937714.296918.5459
102.54050.33060.15675.1461-0.10694.1986-0.0738-0.56480.0120.6186-0.04140.1136-0.1634-0.77620.11520.21970.1404-0.00740.3434-0.02550.011918.0646-37.011461.3114
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 108
2X-RAY DIFFRACTION2L109 - 213
3X-RAY DIFFRACTION3H1 - 120
4X-RAY DIFFRACTION4H121 - 215
5X-RAY DIFFRACTION5F6 - 162
6X-RAY DIFFRACTION6A1 - 108
7X-RAY DIFFRACTION7A109 - 211
8X-RAY DIFFRACTION8B2 - 120
9X-RAY DIFFRACTION9B121 - 214
10X-RAY DIFFRACTION10C7 - 162

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