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- PDB-7uqc: phospho-GlialCAM peptide AA370-389 with Fab MS39p2w174 -

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Basic information

Entry
Database: PDB / ID: 7uqc
Titlephospho-GlialCAM peptide AA370-389 with Fab MS39p2w174
Components
  • (Fab MS39p2w174 ...) x 2
  • Hepatocyte cell adhesion molecule
KeywordsIMMUNE SYSTEM / Autoantigen / EBV / Antibody
Function / homology
Function and homology information


astrocyte end-foot / intracellular protein localization / cell-cell junction / regulation of cell cycle / cell adhesion / axon / plasma membrane / cytoplasm
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...: / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Hepatic and glial cell adhesion molecule
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsLanz, T.V. / Robinson, W.H. / Fernandez, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AR063676 United States
Citation
Journal: To Be Published
Title: Evolution of Antibody Reactivity against EBV EBNA1 to Molecular Mimicry with GlialCAM
Authors: Lanz, T.V. / Robinson, W.H. / Fernandez, D.
#1: Journal: 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
DepositionApr 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 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 MS39p2w174 Light Chain
B: Fab MS39p2w174 Heavy Chain
C: Hepatocyte cell adhesion molecule
G: Fab MS39p2w174 Light Chain
H: Fab MS39p2w174 Heavy Chain
I: Fab MS39p2w174 Light Chain
J: Fab MS39p2w174 Heavy Chain
D: Fab MS39p2w174 Light Chain
E: Fab MS39p2w174 Heavy Chain
F: Hepatocyte cell adhesion molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,41224
Polymers194,79510
Non-polymers61814
Water5,711317
1
A: Fab MS39p2w174 Light Chain
B: Fab MS39p2w174 Heavy Chain
C: Hepatocyte cell adhesion molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9445
Polymers49,8123
Non-polymers1322
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Fab MS39p2w174 Light Chain
H: Fab MS39p2w174 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7276
Polymers47,5852
Non-polymers1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Fab MS39p2w174 Light Chain
J: Fab MS39p2w174 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8237
Polymers47,5852
Non-polymers2385
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Fab MS39p2w174 Light Chain
E: Fab MS39p2w174 Heavy Chain
F: Hepatocyte cell adhesion molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9196
Polymers49,8123
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)195.027, 99.514, 136.414
Angle α, β, γ (deg.)90.000, 112.811, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11H-302-

CL

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Components

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide Hepatocyte cell adhesion molecule / Protein hepaCAM


Mass: 2227.210 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HEPACAM / Production host: Homo sapiens (human) / References: UniProt: Q14CZ8

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Antibody , 2 types, 8 molecules AGIDBHJE

#1: Antibody
Fab MS39p2w174 Light Chain


Mass: 24204.006 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody
Fab MS39p2w174 Heavy Chain


Mass: 23381.055 Da / Num. of mol.: 4
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, 331 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.13 Å3/Da / Density % sol: 60.73 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: tbd

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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 PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2022
RadiationMonochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.65→44.11 Å / Num. obs: 69508 / % possible obs: 98.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 44.71 Å2 / CC1/2: 0.977 / CC star: 0.994 / Rmerge(I) obs: 0.1134 / Rpim(I) all: 0.1134 / Rrim(I) all: 0.1603 / Net I/σ(I): 5.42
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.461 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 10053 / CC1/2: 0.347 / Rpim(I) all: 0.94 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7K7R

7k7r


Resolution: 2.65→44.11 Å / SU ML: 0.3527 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.1734
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2366 3495 5.2 %
Rwork0.1756 63727 -
obs0.1788 67222 95.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.48 Å2
Refinement stepCycle: LAST / Resolution: 2.65→44.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13630 0 22 317 13969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009813958
X-RAY DIFFRACTIONf_angle_d1.279118980
X-RAY DIFFRACTIONf_chiral_restr0.06542103
X-RAY DIFFRACTIONf_plane_restr0.00852447
X-RAY DIFFRACTIONf_dihedral_angle_d11.77791934
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.680.34971210.27222169X-RAY DIFFRACTION81.58
2.68-2.720.34411220.27892508X-RAY DIFFRACTION95.01
2.72-2.760.35811440.27912452X-RAY DIFFRACTION93.52
2.76-2.810.32581400.27442423X-RAY DIFFRACTION90.63
2.81-2.850.35321320.26222480X-RAY DIFFRACTION94.23
2.85-2.90.30211250.252642X-RAY DIFFRACTION98.89
2.9-2.960.31310.24662628X-RAY DIFFRACTION99.14
2.96-3.010.30431360.24832611X-RAY DIFFRACTION98.49
3.01-3.070.38251590.2492577X-RAY DIFFRACTION98.56
3.07-3.140.29771520.22842585X-RAY DIFFRACTION97.54
3.14-3.210.32751540.20952581X-RAY DIFFRACTION97.5
3.21-3.290.26251630.19982549X-RAY DIFFRACTION97.41
3.29-3.380.25881330.19092568X-RAY DIFFRACTION96.91
3.38-3.480.25631480.18622576X-RAY DIFFRACTION97.25
3.48-3.590.27081300.18152474X-RAY DIFFRACTION93.57
3.59-3.720.23261310.17232469X-RAY DIFFRACTION92.2
3.72-3.870.24081470.16352623X-RAY DIFFRACTION98.61
3.87-4.050.21931550.15082639X-RAY DIFFRACTION98.8
4.05-4.260.1921400.13982590X-RAY DIFFRACTION98.34
4.26-4.530.15371510.11992601X-RAY DIFFRACTION98.04
4.53-4.880.16961610.11862582X-RAY DIFFRACTION96.99
4.88-5.370.16841040.12692477X-RAY DIFFRACTION91.95
5.37-6.140.20211540.15052608X-RAY DIFFRACTION96.98
6.14-7.730.20521330.1592675X-RAY DIFFRACTION98.73
7.73-44.110.17661290.14562640X-RAY DIFFRACTION95.35

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