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- PDB-9npg: X-ray crystal structure of recombinant Can f 1-C100S in complex w... -

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Basic information

Entry
Database: PDB / ID: 9npg
TitleX-ray crystal structure of recombinant Can f 1-C100S in complex with human IgE mAb 12F3 Fab
Components
  • IgE 12F3 Fab heavy chain
  • IgE 12F3 Fab light chain
  • Major allergen Can f 1
KeywordsALLERGEN/IMMUNE SYSTEM / Can f 1-IgE / dog allergen / allergen-antibody complex / human antibody / IgE-Can f 1 complex / allergen-antibody interaction / ALLERGEN / ALLERGEN-IMMUNE SYSTEM complex
Function / homologyvon Ebner's gland protein/ Bos/Can allergen / Lipocalin / small molecule binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / extracellular space / Major allergen Can f 1
Function and homology information
Biological speciesHomo sapiens (human)
Canis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å
AuthorsKhatri, K. / Ball, A. / Smith, S.A. / Champan, M.D. / Pomes, A. / Chruszcz, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI077653-14 United States
CitationJournal: Protein Sci. / Year: 2025
Title: Human IgE monoclonal antibodies define two unusual epitopes trapping dog allergen Can f 1 in different conformations.
Authors: Khatri, K. / Ball, A. / Glesner, J. / Linn, C. / Vailes, L.D. / Wunschmann, S. / Gabel, S.A. / Zhang, J. / Peebles Jr., R.S. / Borowski, T. / Mueller, G.A. / Chapman, M.D. / Smith, S.A. / ...Authors: Khatri, K. / Ball, A. / Glesner, J. / Linn, C. / Vailes, L.D. / Wunschmann, S. / Gabel, S.A. / Zhang, J. / Peebles Jr., R.S. / Borowski, T. / Mueller, G.A. / Chapman, M.D. / Smith, S.A. / Pomes, A. / Chruszcz, M.
History
DepositionMar 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IgE 12F3 Fab heavy chain
B: IgE 12F3 Fab light chain
C: Major allergen Can f 1
D: IgE 12F3 Fab heavy chain
E: IgE 12F3 Fab light chain
F: Major allergen Can f 1
G: IgE 12F3 Fab heavy chain
H: IgE 12F3 Fab light chain
K: IgE 12F3 Fab heavy chain
J: IgE 12F3 Fab light chain
L: Major allergen Can f 1
I: Major allergen Can f 1


Theoretical massNumber of molelcules
Total (without water)258,17712
Polymers258,17712
Non-polymers00
Water1,72996
1
A: IgE 12F3 Fab heavy chain
B: IgE 12F3 Fab light chain
C: Major allergen Can f 1


Theoretical massNumber of molelcules
Total (without water)64,5443
Polymers64,5443
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-33 kcal/mol
Surface area25400 Å2
MethodPISA
2
D: IgE 12F3 Fab heavy chain
E: IgE 12F3 Fab light chain
F: Major allergen Can f 1


Theoretical massNumber of molelcules
Total (without water)64,5443
Polymers64,5443
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-34 kcal/mol
Surface area26310 Å2
MethodPISA
3
G: IgE 12F3 Fab heavy chain
H: IgE 12F3 Fab light chain
I: Major allergen Can f 1


Theoretical massNumber of molelcules
Total (without water)64,5443
Polymers64,5443
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-34 kcal/mol
Surface area25640 Å2
MethodPISA
4
K: IgE 12F3 Fab heavy chain
J: IgE 12F3 Fab light chain
L: Major allergen Can f 1


Theoretical massNumber of molelcules
Total (without water)64,5443
Polymers64,5443
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-32 kcal/mol
Surface area25830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.407, 191.156, 88.187
Angle α, β, γ (deg.)90.00, 102.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
IgE 12F3 Fab heavy chain


Mass: 24638.535 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody
IgE 12F3 Fab light chain


Mass: 23392.988 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein
Major allergen Can f 1 / Allergen Dog 1


Mass: 16512.646 Da / Num. of mol.: 4 / Mutation: C118S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Production host: Escherichia coli (E. coli) / References: UniProt: O18873
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
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: 2.63 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2 M NaCl, 0.1 M sodium citrate tribasic dihydrate pH 4.2, 20% w/v PEG 8,000 conditions

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Nov 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.12→40 Å / Num. obs: 46837 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.976 / CC star: 0.994 / Rmerge(I) obs: 0.257 / Rpim(I) all: 0.104 / Rrim(I) all: 0.278 / Net I/σ(I): 7.47
Reflection shellResolution: 3.12→3.17 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 1.97 / Num. unique obs: 2313 / CC1/2: 0.598 / CC star: 0.865 / Rpim(I) all: 0.314 / Rrim(I) all: 0.813 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.12→39.67 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.877 / SU B: 53.438 / SU ML: 0.425 / Cross valid method: THROUGHOUT / ESU R Free: 0.488 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24488 2298 4.9 %RANDOM
Rwork0.20318 ---
obs0.20524 44368 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 83.621 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å2-0 Å21.71 Å2
2---2.06 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 3.12→39.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17418 0 0 96 17514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01217796
X-RAY DIFFRACTIONr_bond_other_d0.0010.01616375
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.81424227
X-RAY DIFFRACTIONr_angle_other_deg0.4551.73237853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49552294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.191580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.904102825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.060.22772
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0220934
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023914
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_it1.3382.2559224
X-RAY DIFFRACTIONr_mcbond_other1.3372.2559224
X-RAY DIFFRACTIONr_mcangle_it2.3754.04611502
X-RAY DIFFRACTIONr_mcangle_other2.3754.04611503
X-RAY DIFFRACTIONr_scbond_it1.2862.3078572
X-RAY DIFFRACTIONr_scbond_other1.2862.3078573
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2514.19912726
X-RAY DIFFRACTIONr_long_range_B_refined5.38326.6469233
X-RAY DIFFRACTIONr_long_range_B_other5.3826.6469221
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.12→3.201 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 148 -
Rwork0.29 3266 -
obs--99.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.8354-0.02591.18795.19150.78694.2593-0.26770.0662-0.0667-0.73130.33310.4767-0.4653-0.336-0.06530.2307-0.0102-0.16050.6849-0.10220.3586-11.15654.03216.957
20.57191.01930.3573.08192.13852.06570.0229-0.0486-0.01130.0405-0.0017-0.0570.0707-0.0814-0.02120.1755-0.0116-0.11770.4618-0.0620.2402-4.44754.02622.181
31.1669-0.6282-0.52281.06380.06739.0616-0.0374-0.0515-0.1979-0.04070.10250.19130.0086-0.5556-0.06510.0377-0.0538-0.05930.3552-0.06650.3102-24.07928.14939.464
40.69550.5566-0.50362.3926-0.77160.44760.1833-0.14690.05810.2585-0.13070.0571-0.12790.1734-0.05260.2976-0.0793-0.13970.5222-0.07990.1305-7.06551.9943.021
525.1555-12.84154.558931.38948.20449.93820.11610.5562-0.43571.8499-0.3062-0.0445-0.47871.51330.19010.5429-0.3062-0.17250.778-0.04110.1088-4.66834.27449.137
60.8825-2.1073-2.89038.97554.330311.4542-0.3123-0.28170.0640.44070.4019-0.28851.23251.4543-0.08970.23880.1865-0.16140.5409-0.05110.2293-7.9224.30746.913
712.01918.228-3.17558.8098-6.10748.14890.6503-0.49710.89620.8872-0.53880.5491-0.87731.1257-0.11150.2448-0.0475-0.00930.3063-0.10040.25178.61385.57430.772
813.59937.9855-2.36959.84453.01764.19030.4928-0.07740.8280.8259-0.07110.16310.33270.0018-0.42170.2788-0.0485-0.10630.288-0.02910.26994.71188.66637.017
92.21980.29910.75083.8712-1.05562.87130.00020.27060.07550.0607-0.0316-0.272-0.00590.14150.03140.0596-0.0394-0.09220.3557-0.03120.19157.71684.93424.995
101.55892.78151.151816.94463.54453.5995-0.07180.0975-0.1981.29280.12160.56360.1215-0.5462-0.04990.1715-0.00670.10920.3749-0.06280.2792-53.55.66923.436
111.3156-1.6049-0.97973.72171.21962.21850.01970.01780.05260.4516-0.1798-0.0021-0.017-0.05760.16010.22560.0152-0.13590.3654-0.0290.2807-44.5084.55922.028
123.9647-1.7413-2.18992.8350.52855.8792-0.05220.31010.24870.2984-0.00410.52510.142-0.40990.05630.1551-0.0074-0.06680.3742-0.04790.4945-54.40931.44-2.469
130.31130.1194-0.56143.2024-0.63363.3241-0.07260.15110.0049-0.20740.0207-0.23730.18580.02850.05190.17880.0081-0.13660.2899-0.03760.2056-35.981-1.4284.167
140.0994-0.630.23744.5428-1.6310.6220.00370.02670.01010.1047-0.0156-0.1873-0.0062-0.05380.01190.05690.0288-0.11460.3815-0.03190.3125-38.58722.028-0.599
153.5391-6.9427-2.811419.94818.34643.5730.0472-0.17340.3317-0.13240.2606-0.5723-0.02750.2419-0.30780.0602-0.0001-0.10390.3612-0.00910.345-34.96940.163-7.461
162.1785-2.6691.92364.3965-3.45567.20180.1310.0312-0.2447-0.3390.116-0.14530.09630.0713-0.2470.29880.0107-0.06710.2487-0.02740.3634-32.137-27.74915.344
178.47271.8067-2.57291.45020.3012.4051-0.2328-0.1918-0.2140.0858-0.00720.06050.70540.18120.240.44690.0696-0.06310.25870.03360.1551-40.4-30.71918.619
180.88290.99120.04932.2984-0.33723.13290.1204-0.3046-0.13370.2669-0.1459-0.50070.04150.21030.02550.21880.0735-0.17120.36830.03410.2615-29.851-25.60425.704
190.4988-1.3713-0.05223.78650.30491.9276-0.1312-0.10150.05790.37420.3032-0.2022-0.12840.1236-0.1720.12860.0593-0.15180.4499-0.0890.2923-6.559-0.2221.54
200.9551.67181.506911.68670.32234.69030.18310.16710.04130.1908-0.043-0.5629-0.6681-0.2418-0.14010.54510.34440.06920.47250.06180.5972-10.96631.912-6.124
211.8899-0.7693-1.19681.2986-0.06333.9614-0.03520.27530.05940.094-0.14350.2681-0.0357-0.49280.17880.0795-0.0128-0.09390.4696-0.06830.321-15.28425.687-2.648
222.107-1.0108-1.06621.8529-0.144510.3780.168-0.09560.3749-0.3224-0.1657-0.76120.22810.2708-0.00230.13050.02460.0130.30860.01980.52759.702-3.2882.591
231.6853-2.10761.87163.8501-2.66613.36580.0788-0.03250.1673-0.19710.0134-0.24280.12050.0463-0.09220.04430.0243-0.07030.4154-0.11840.28361.071-6.7583.582
241.3776-0.9412-0.28086.78884.05585.18640.0409-0.14990.0653-0.104-0.0069-0.2512-0.09780.2758-0.0340.034-0.0082-0.07420.46230.01810.20481.34328.409-3.869
255.1937-1.08573.4071.9111-1.21627.17260.11360.3338-0.2922-0.38710.2111-0.41270.89720.5543-0.32470.34730.0712-0.0990.2759-0.11240.34610.534-33.63414.771
2618.6138-10.4308-10.844311.27942.787211.2925-0.3011-0.16120.6904-0.3560.8224-0.13140.67230.2148-0.52130.28020.0049-0.20250.3146-0.01680.1757-0.113-33.92715.72
272.03920.38710.15893.4746-2.91662.7584-0.17-0.0417-0.08570.22750.0757-0.3369-0.03760.06680.09430.24430.1923-0.19360.4745-0.13380.19569.218-31.01724.542
287.59232.4147-5.43113.489-2.46284.74820.3649-0.4412-0.39090.2745-0.6954-0.4953-0.26450.82450.33050.26840.064-0.24230.55040.05990.2653-39.04364.77543.313
290.4050.8766-0.27154.1213-1.59230.6416-0.13130.0073-0.01810.17330.0553-0.1202-0.1364-0.05640.0760.32360.0431-0.16470.3872-0.0470.1796-48.21661.7642.129
300.8736-1.5531-0.73676.35071.53132.9986-0.07330.12290.0120.2074-0.0789-0.18550.08010.02750.15220.0374-0.0263-0.07970.34180.01080.2231-50.51530.52447.304
310.72660.44790.29132.1019-0.12420.94570.02750.0854-0.0537-0.2659-0.138-0.31020.19110.06320.11050.3004-0.0289-0.07130.3391-0.03730.1865-45.79761.03220.33
324.39910.798-6.6663.77612.929123.9067-0.04310.2166-0.4359-0.042-0.35570.29370.5118-2.55040.39880.0454-0.0337-0.07410.591-0.03490.245-63.90129.58244.548
330.43260.4202-0.61552.78431.544611.0251-0.0789-0.0927-0.1477-0.7172-0.19410.3265-0.7079-1.13020.2730.2420.1597-0.17920.477-0.13230.3359-64.42835.51537.797
346.63442.6781-2.45066.89620.01552.1808-0.0087-0.69060.15781.1009-0.0963-0.9547-0.20990.40930.1050.5876-0.1332-0.44750.4756-0.00120.3709-33.5692.57832.474
3522.81684.6135.41673.89963.39315.06260.1725-0.58020.78930.514-0.35930.2501-0.42190.0260.18670.5052-0.1475-0.03870.1908-0.04340.1524-38.38797.45135.638
361.7438-0.74140.28112.8008-1.43313.92460.13630.1151-0.02590.2419-0.1466-0.4104-0.55430.63030.01030.2487-0.1215-0.18640.38040.00790.2627-33.2391.81923.699
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 32
2X-RAY DIFFRACTION2A33 - 126
3X-RAY DIFFRACTION3A127 - 224
4X-RAY DIFFRACTION4B1 - 142
5X-RAY DIFFRACTION5B143 - 148
6X-RAY DIFFRACTION6B149 - 213
7X-RAY DIFFRACTION7C11 - 31
8X-RAY DIFFRACTION8C32 - 62
9X-RAY DIFFRACTION9C63 - 153
10X-RAY DIFFRACTION10D1 - 30
11X-RAY DIFFRACTION11D31 - 126
12X-RAY DIFFRACTION12D127 - 225
13X-RAY DIFFRACTION13E1 - 69
14X-RAY DIFFRACTION14E70 - 187
15X-RAY DIFFRACTION15E188 - 212
16X-RAY DIFFRACTION16F12 - 56
17X-RAY DIFFRACTION17F57 - 88
18X-RAY DIFFRACTION18F89 - 153
19X-RAY DIFFRACTION19G1 - 127
20X-RAY DIFFRACTION20G128 - 144
21X-RAY DIFFRACTION21G145 - 224
22X-RAY DIFFRACTION22H1 - 30
23X-RAY DIFFRACTION23H31 - 108
24X-RAY DIFFRACTION24H109 - 214
25X-RAY DIFFRACTION25I12 - 60
26X-RAY DIFFRACTION26I61 - 74
27X-RAY DIFFRACTION27I75 - 153
28X-RAY DIFFRACTION28J1 - 35
29X-RAY DIFFRACTION29J36 - 122
30X-RAY DIFFRACTION30J123 - 213
31X-RAY DIFFRACTION31K1 - 127
32X-RAY DIFFRACTION32K128 - 148
33X-RAY DIFFRACTION33K149 - 225
34X-RAY DIFFRACTION34L11 - 42
35X-RAY DIFFRACTION35L43 - 66
36X-RAY DIFFRACTION36L67 - 153

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  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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