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- PDB-7k7r: EBNA1 peptide AA386-405 with Fab MS39p2w174 -

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Basic information

Entry
Database: PDB / ID: 7k7r
TitleEBNA1 peptide AA386-405 with Fab MS39p2w174
Components
  • EBNA1 peptide AA386-405
  • Fab HC MS39p2w174
  • Fab LC MS39p2w174
KeywordsIMMUNE SYSTEM / Autoantigen / EBV / Antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
Human gammaherpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsLanz, T.V. / Robinson, W.H. / Jude, K.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nature / Year: 2022
Title: Clonally expanded B cells in multiple sclerosis bind EBV EBNA1 and GlialCAM.
Authors: Lanz, T.V. / Brewer, R.C. / Ho, P.P. / Moon, J.S. / Jude, K.M. / Fernandez, D. / Fernandes, R.A. / Gomez, A.M. / Nadj, G.S. / Bartley, C.M. / Schubert, R.D. / Hawes, I.A. / Vazquez, S.E. / ...Authors: Lanz, T.V. / Brewer, R.C. / Ho, P.P. / Moon, J.S. / Jude, K.M. / Fernandez, D. / Fernandes, R.A. / Gomez, A.M. / Nadj, G.S. / Bartley, C.M. / Schubert, R.D. / Hawes, I.A. / Vazquez, S.E. / Iyer, M. / Zuchero, J.B. / Teegen, B. / Dunn, J.E. / Lock, C.B. / Kipp, L.B. / Cotham, V.C. / Ueberheide, B.M. / Aftab, B.T. / Anderson, M.S. / DeRisi, J.L. / Wilson, M.R. / Bashford-Rogers, R.J.M. / Platten, M. / Garcia, K.C. / Steinman, L. / Robinson, W.H.
History
DepositionSep 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab LC MS39p2w174
B: Fab HC MS39p2w174
C: EBNA1 peptide AA386-405
D: Fab LC MS39p2w174
E: Fab HC MS39p2w174
F: EBNA1 peptide AA386-405
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,02611
Polymers100,6226
Non-polymers4045
Water43224
1
A: Fab LC MS39p2w174
B: Fab HC MS39p2w174
C: EBNA1 peptide AA386-405


Theoretical massNumber of molelcules
Total (without water)50,3113
Polymers50,3113
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Fab LC MS39p2w174
E: Fab HC MS39p2w174
F: EBNA1 peptide AA386-405
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7158
Polymers50,3113
Non-polymers4045
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.657, 137.562, 178.996
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 23 or (resid 24...
21chain D
12chain B
22(chain E and (resid 2 through 131 or resid 136 through 217))
13(chain C and resid 389 through 400)
23chain F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPCYSCYS(chain A and (resid 1 through 23 or (resid 24...AA1 - 231 - 23
121ARGARGARGARG(chain A and (resid 1 through 23 or (resid 24...AA2424
131ASPASPGLYGLY(chain A and (resid 1 through 23 or (resid 24...AA1 - 2171 - 217
211ASPASPGLYGLYchain DDD1 - 2171 - 217
112VALVALLYSLYSchain BBB2 - 2172 - 217
212VALVALSERSER(chain E and (resid 2 through 131 or resid 136 through 217))EE2 - 1312 - 131
222GLYGLYLYSLYS(chain E and (resid 2 through 131 or resid 136 through 217))EE136 - 217136 - 217
113SERSERPROPRO(chain C and resid 389 through 400)CC389 - 4004 - 15
213SERSERPROPROchain FFF389 - 4004 - 15

NCS ensembles :
ID
1
2
3

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Components

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide EBNA1 peptide AA386-405


Mass: 2141.352 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Human gammaherpesvirus 4 (Epstein-Barr virus)

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Antibody , 2 types, 4 molecules ADBE

#1: Antibody Fab LC MS39p2w174


Mass: 24204.006 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Fab HC MS39p2w174


Mass: 23965.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 29 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.7 Å3/Da / Density % sol: 66.79 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: Fab (15 mg/ml) mixed with peptide at a 1:7.5 molar ratio. 0.48M Sodium Citrate, 0.72M Sodium/Potassium Phosphate, 3% MPD (v/v), 0.1M HEPES, pH 6.9.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: May 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.19→45.14 Å / Num. obs: 51233 / % possible obs: 96.1 % / Redundancy: 3.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.101 / Rrim(I) all: 0.186 / Net I/σ(I): 5.5 / Num. measured all: 231612 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.19-2.2425.921743036370.1264.9727.7760.178
10.73-45.143.10.02420586710.9990.0160.02931.794.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.95 Å39.4 Å
Translation2.95 Å39.4 Å

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless3.3.22data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
XDS20200131data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LRI

4lri


Resolution: 2.5→45.14 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.4 / Stereochemistry target values: ML
Details: Data were initially processed to 2.19 A resolution, but in final paired refinement tests we found 2.5 A to be the highest useful resolution
RfactorNum. reflection% reflection
Rfree0.2522 1912 5.23 %
Rwork0.2109 34662 -
obs0.2131 36574 71.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 178.5 Å2 / Biso mean: 56.3739 Å2 / Biso min: 17.22 Å2
Refinement stepCycle: final / Resolution: 2.5→45.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6778 0 25 24 6827
Biso mean--73.27 37.72 -
Num. residues----891
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2030X-RAY DIFFRACTION11.872TORSIONAL
12D2030X-RAY DIFFRACTION11.872TORSIONAL
21B1893X-RAY DIFFRACTION11.872TORSIONAL
22E1893X-RAY DIFFRACTION11.872TORSIONAL
31C114X-RAY DIFFRACTION11.872TORSIONAL
32F114X-RAY DIFFRACTION11.872TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.560.4192630.32461256131937
2.56-2.630.4308760.30981389146541
2.63-2.710.3708880.28911514160244
2.71-2.80.3517960.29591664176049
2.8-2.90.29341020.28671862196454
2.9-3.010.34361180.30192026214459
3.01-3.150.32071050.27752279238465
3.15-3.320.331420.26312589273175
3.32-3.520.27111560.23792946310285
3.52-3.80.25691940.21773265345995
3.8-4.180.24931930.19133429362298
4.18-4.780.18641880.15343427361598
4.78-6.020.20571730.16053507368099
6.02-45.140.20952180.19083509372797
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)
12.0661-0.3004-0.59550.47610.21141.26230.01420.19990.1935-0.0144-0.1060.0686-0.2524-0.22460.10850.2421-0.0121-0.09040.53310.02570.2449-19.9996-30.2213-39.2428
21.7168-0.0382-0.24150.54310.43510.68670.0126-0.1202-0.00910.039-0.09740.0062-0.0982-0.1980.08780.2222-0.0006-0.04910.45620.03110.183-7.7707-37.6824-27.8662
33.1926-2.6446-3.19565.5771-0.3075.760.42350.76660.1145-0.67430.1725-0.5737-0.27150.0032-0.45920.2674-0.03840.05870.89630.0020.349414.6988-36.7622-52.1522
41.38810.20490.60141.3362-0.9222.88710.09930.3784-0.3885-0.61430.279-0.08271.0243-0.1285-0.19150.6092-0.187-0.09350.4212-0.06090.297624.1293-49.8639-27.173
51.0102-0.24050.81741.4962-0.69343.17080.0603-0.4117-0.7096-0.30350.48530.41851.004-0.5007-0.19080.4346-0.2343-0.25170.490.18670.322214.1166-53.9707-12.6179
62.43610.2429-2.64841.5631-0.49122.9183-0.531-1.35162.42480.0263-0.3663-0.4934-0.53150.00840.54190.72220.0289-0.21780.5437-0.10960.795418.9047-22.7551-2.1831
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A'A1 - 217
2X-RAY DIFFRACTION2chain 'B'B2 - 217
3X-RAY DIFFRACTION3chain 'C'C389 - 402
4X-RAY DIFFRACTION4chain 'D'D1 - 217
5X-RAY DIFFRACTION5chain 'E'E1 - 219
6X-RAY DIFFRACTION6chain 'F'F389 - 400

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