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- PDB-5ifj: Crystal structure of anti-gliadin 1002-1E01 Fab fragment in compl... -

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Basic information

Entry
Database: PDB / ID: 5ifj
TitleCrystal structure of anti-gliadin 1002-1E01 Fab fragment in complex of peptide PLQPEQPFP
Components
  • 1E01 Fab fragment heavy chain
  • 1E01 Fab fragment light chain
  • peptide PRO-LEU-GLN-PRO-GLU-GLN-PRO-PHE-PRO
KeywordsIMMUNE SYSTEM / anti-gliadin antibody / gliadin peptide / celiac disease
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
Triticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSnir, O. / Chen, X. / Gidoni, M. / du Pre, M.F. / Zhao, Y. / Steinsbo, O. / Lundin, K.E. / Yaari, G. / Sollid, L.M.
CitationJournal: JCI Insight / Year: 2017
Title: Stereotyped antibody responses target posttranslationally modified gluten in celiac disease.
Authors: Snir, O. / Chen, X. / Gidoni, M. / du Pre, M.F. / Zhao, Y. / Steinsbo, O. / Lundin, K.E. / Yaari, G. / Sollid, L.M.
History
DepositionFeb 26, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Dec 6, 2017Group: Database references / Structure summary / Category: audit_author / citation_author
Revision 1.3Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Sep 17, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1E01 Fab fragment heavy chain
B: 1E01 Fab fragment light chain
C: peptide PRO-LEU-GLN-PRO-GLU-GLN-PRO-PHE-PRO
D: 1E01 Fab fragment heavy chain
E: 1E01 Fab fragment light chain
F: peptide PRO-LEU-GLN-PRO-GLU-GLN-PRO-PHE-PRO
G: 1E01 Fab fragment heavy chain
H: 1E01 Fab fragment light chain
I: peptide PRO-LEU-GLN-PRO-GLU-GLN-PRO-PHE-PRO
J: 1E01 Fab fragment heavy chain
K: 1E01 Fab fragment light chain
L: peptide PRO-LEU-GLN-PRO-GLU-GLN-PRO-PHE-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,43324
Polymers191,28012
Non-polymers1,15312
Water6,539363
1
A: 1E01 Fab fragment heavy chain
B: 1E01 Fab fragment light chain
C: peptide PRO-LEU-GLN-PRO-GLU-GLN-PRO-PHE-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,49310
Polymers47,8203
Non-polymers6727
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 1E01 Fab fragment heavy chain
E: 1E01 Fab fragment light chain
F: peptide PRO-LEU-GLN-PRO-GLU-GLN-PRO-PHE-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9164
Polymers47,8203
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: 1E01 Fab fragment heavy chain
H: 1E01 Fab fragment light chain
I: peptide PRO-LEU-GLN-PRO-GLU-GLN-PRO-PHE-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1086
Polymers47,8203
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: 1E01 Fab fragment heavy chain
K: 1E01 Fab fragment light chain
L: peptide PRO-LEU-GLN-PRO-GLU-GLN-PRO-PHE-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9164
Polymers47,8203
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.450, 141.280, 177.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody
1E01 Fab fragment heavy chain


Mass: 23765.488 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody
1E01 Fab fragment light chain


Mass: 23002.445 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide
peptide PRO-LEU-GLN-PRO-GLU-GLN-PRO-PHE-PRO


Mass: 1052.177 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Triticum aestivum (bread wheat)
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 3.73 Å3/Da / Density % sol: 67.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium Sulphate, 0.1M MES, pH 6.5, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.35→112.45 Å / Num. obs: 117865 / % possible obs: 100 % / Redundancy: 13.5 % / Net I/σ(I): 15.9
Reflection shellResolution: 2.35→2.41 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IHZ

5ihz


Resolution: 2.35→88.53 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.28
RfactorNum. reflection% reflection
Rfree0.2409 5827 4.95 %
Rwork0.205 --
obs0.2067 117758 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→88.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13068 0 60 363 13491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413445
X-RAY DIFFRACTIONf_angle_d0.90418310
X-RAY DIFFRACTIONf_dihedral_angle_d14.7847996
X-RAY DIFFRACTIONf_chiral_restr0.0512051
X-RAY DIFFRACTIONf_plane_restr0.0062323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.37670.36861920.32493687X-RAY DIFFRACTION100
2.3767-2.40470.36171730.30993729X-RAY DIFFRACTION100
2.4047-2.4340.33721780.30163714X-RAY DIFFRACTION100
2.434-2.46480.35191860.29113656X-RAY DIFFRACTION100
2.4648-2.49720.3311820.28933737X-RAY DIFFRACTION100
2.4972-2.53150.3171860.2823692X-RAY DIFFRACTION100
2.5315-2.56760.34312110.29093660X-RAY DIFFRACTION100
2.5676-2.6060.37012170.29523682X-RAY DIFFRACTION100
2.606-2.64670.30682210.29613641X-RAY DIFFRACTION100
2.6467-2.69010.31511970.27173737X-RAY DIFFRACTION100
2.6901-2.73650.31951900.26913689X-RAY DIFFRACTION100
2.7365-2.78620.35711940.26373664X-RAY DIFFRACTION100
2.7862-2.83980.30462030.24733730X-RAY DIFFRACTION100
2.8398-2.89780.29541710.2423710X-RAY DIFFRACTION100
2.8978-2.96080.26131940.23443726X-RAY DIFFRACTION100
2.9608-3.02970.34141980.24963684X-RAY DIFFRACTION100
3.0297-3.10540.27652330.25193682X-RAY DIFFRACTION100
3.1054-3.18940.29461810.24113723X-RAY DIFFRACTION100
3.1894-3.28330.30511990.24913756X-RAY DIFFRACTION100
3.2833-3.38920.26831800.22593696X-RAY DIFFRACTION100
3.3892-3.51040.25571930.20953739X-RAY DIFFRACTION100
3.5104-3.65090.2431840.20613727X-RAY DIFFRACTION100
3.6509-3.81710.24112040.20353750X-RAY DIFFRACTION100
3.8171-4.01830.24641790.19333784X-RAY DIFFRACTION100
4.0183-4.27010.19781720.16713758X-RAY DIFFRACTION100
4.2701-4.59980.19522050.15163740X-RAY DIFFRACTION100
4.5998-5.06260.16431860.14463801X-RAY DIFFRACTION100
5.0626-5.79510.18292150.15623780X-RAY DIFFRACTION100
5.7951-7.30070.21562010.18413847X-RAY DIFFRACTION100
7.3007-88.59280.17382020.18224010X-RAY DIFFRACTION100
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)
10.97070.32460.44880.98720.36691.511-0.0173-0.0625-0.1774-0.05510.0047-0.04370.01650.0480.03090.36210.07380.00070.36810.08820.4340.2567-45.675218.752
21.37110.12970.73371.62050.20852.4438-0.04720.0891-0.0645-0.07580.01350.1672-0.0456-0.07870.04250.40680.0699-0.02030.39890.0650.4062-3.7271-31.54449.1047
31.49210.54530.7471.0321.04691.5942-0.0084-0.0892-0.1401-0.0246-0.0802-0.01230.07610.0770.07960.38990.04770.14330.36270.11120.443224.4069-65.373615.9584
41.89060.6030.28851.26140.58291.9688-0.0226-0.3025-0.3037-0.0615-0.0567-0.15320.04680.14270.07390.35460.01420.11650.37510.06410.418740.0681-62.55488.4207
53.03260.2392-1.84322.2593-0.80483.5494-0.42650.1141-0.4979-0.25440.0648-0.03740.7638-0.07790.3180.5166-0.04970.02020.35410.07850.386210.9985-67.642945.3582
62.16070.1896-1.29623.2382-1.76544.1848-0.28720.0462-0.3474-0.3348-0.4032-0.71530.95670.56670.60460.67960.05770.07880.4470.12620.493614.4853-75.01961.2559
71.8025-0.8957-0.00921.78850.11512.1130.0297-0.2029-0.45590.1122-0.01780.36160.3509-0.2671-0.01440.4119-0.10380.04230.41030.09950.7352-9.252-76.135322.9051
81.9599-1.51-0.03262.66110.61951.9980.0378-0.1925-0.8359-0.00810.08730.90980.6426-0.8065-0.08830.6757-0.280.01680.8130.17711.2272-24.0445-85.736424.2309
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1:220)
2X-RAY DIFFRACTION2(chain B and resseq 1:213)
3X-RAY DIFFRACTION3(chain D and resseq 1:221)
4X-RAY DIFFRACTION4(chain E and resseq 1:213)
5X-RAY DIFFRACTION5(chain G and resseq 1:221)
6X-RAY DIFFRACTION6(chain H and resseq 1:213)
7X-RAY DIFFRACTION7(chain J and resseq 1:223)
8X-RAY DIFFRACTION8(chain K and resseq 1:213)

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