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- PDB-7vac: Crystal structure of antibody 14A in complex with MUC1 glycopepti... -

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Basic information

Entry
Database: PDB / ID: 7vac
TitleCrystal structure of antibody 14A in complex with MUC1 glycopeptide(GlycoST)
Components
  • 14A fab heavy chain
  • 14A fab light chain
  • Mucin-1 subunit alpha
KeywordsIMMUNE SYSTEM / Antibody / anti-MUC1 / Glycopeptide / PEPTIDE BINDING PROTEIN
Function / homology
Function and homology information


Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / negative regulation of cell adhesion mediated by integrin / negative regulation of transcription by competitive promoter binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Dectin-2 family / mitotic G1 DNA damage checkpoint signaling ...Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / negative regulation of cell adhesion mediated by integrin / negative regulation of transcription by competitive promoter binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Dectin-2 family / mitotic G1 DNA damage checkpoint signaling / transcription coregulator activity / DNA damage response, signal transduction by p53 class mediator / Golgi lumen / p53 binding / Interleukin-4 and Interleukin-13 signaling / vesicle / apical plasma membrane / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / nucleus / plasma membrane
Similarity search - Function
Domain found in sea urchin sperm protein, enterokinase, agrin / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-beta-D-galactopyranose / Mucin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsNiu, J. / Xu, L. / Meng, B. / Han, Y.B. / Yang, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Site-specific GalNAc modification on a MUC1 neoantigen epitope forms a basis for high-affinity antibody binding
Authors: Han, Y.B. / Xu, L.
History
DepositionAug 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 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: 14A fab light chain
B: 14A fab heavy chain
C: 14A fab light chain
D: 14A fab heavy chain
E: 14A fab light chain
F: 14A fab heavy chain
G: Mucin-1 subunit alpha
H: Mucin-1 subunit alpha
I: Mucin-1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,22215
Polymers147,8949
Non-polymers1,3276
Water00
1
A: 14A fab light chain
B: 14A fab heavy chain
G: Mucin-1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7415
Polymers49,2983
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-27 kcal/mol
Surface area19460 Å2
MethodPISA
2
C: 14A fab light chain
D: 14A fab heavy chain
H: Mucin-1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7415
Polymers49,2983
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-28 kcal/mol
Surface area19070 Å2
MethodPISA
3
E: 14A fab light chain
F: 14A fab heavy chain
I: Mucin-1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7415
Polymers49,2983
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-25 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.920, 206.848, 225.405
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 2 through 215)
21chain C
31(chain E and resid 2 through 215)
12(chain B and (resid 2 through 132 or resid 138 through 217))
22(chain D and (resid 2 through 132 or resid 138 through 217))
32chain F
13(chain G and (resid 6 through 201 or resid 301))
23(chain H and resid 6 through 301)
33chain I

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and resid 2 through 215)A2 - 215
211chain CC2 - 215
311(chain E and resid 2 through 215)E2 - 215
112(chain B and (resid 2 through 132 or resid 138 through 217))B2 - 132
122(chain B and (resid 2 through 132 or resid 138 through 217))B138 - 217
212(chain D and (resid 2 through 132 or resid 138 through 217))D2 - 132
222(chain D and (resid 2 through 132 or resid 138 through 217))D138 - 217
312chain FF2 - 217
113(chain G and (resid 6 through 201 or resid 301))G0
213(chain H and resid 6 through 301)H6 - 301
313chain II6 - 301

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody 14A fab light chain


Mass: 23512.129 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichopalpus nigribasis (fry)
#2: Antibody 14A fab heavy chain


Mass: 24568.670 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichopalpus nigribasis (fry)
#3: Protein/peptide Mucin-1 subunit alpha / MUC1 peptide


Mass: 1217.334 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P15941
#4: Sugar
ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
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: 3.38 Å3/Da / Density % sol: 63.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Sodium citrate pH 5.5, Isopropanol 10%, PEG 4000 20%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.5→40.69 Å / Num. obs: 26442 / % possible obs: 99.7 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rpim(I) all: 0.048 / Rrim(I) all: 0.164 / Net I/σ(I): 11.7
Reflection shellResolution: 3.5→3.63 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 2588 / CC1/2: 0.816 / Rpim(I) all: 0.253 / Rrim(I) all: 0.841

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YHY

4yhy


Resolution: 3.5→40.69 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.219 1260 4.77 %
Rwork0.1711 25182 -
obs0.1734 26442 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.7 Å2 / Biso mean: 55.4481 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 3.5→40.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9929 0 168 0 10097
Biso mean--77.05 --
Num. residues----1319
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1938X-RAY DIFFRACTION9.463TORSIONAL
12C1938X-RAY DIFFRACTION9.463TORSIONAL
13E1938X-RAY DIFFRACTION9.463TORSIONAL
21B1893X-RAY DIFFRACTION9.463TORSIONAL
22D1893X-RAY DIFFRACTION9.463TORSIONAL
23F1893X-RAY DIFFRACTION9.463TORSIONAL
31G74X-RAY DIFFRACTION9.463TORSIONAL
32H74X-RAY DIFFRACTION9.463TORSIONAL
33I74X-RAY DIFFRACTION9.463TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.640.25751490.21192724287399
3.64-3.810.26161260.20327212847100
3.81-4.010.28621500.188727402890100
4.01-4.260.20941350.168627952930100
4.26-4.580.1571240.145227372861100
4.58-5.050.20161380.128727802918100
5.05-5.770.21081410.15628132954100
5.77-7.270.21771460.186428713017100
7.27-40.690.21161510.182430013152100
Refinement TLS params.Method: refined / Origin x: 27.5567 Å / Origin y: -46.789 Å / Origin z: -32.9233 Å
111213212223313233
T0.2156 Å20.015 Å2-0.0124 Å2-0.3431 Å2-0.0059 Å2--0.2902 Å2
L0.3076 °20.0268 °20.072 °2-0.7071 °20.0805 °2--0.4312 °2
S0.0173 Å °0.1016 Å °0.025 Å °-0.1799 Å °-0.0499 Å °0.0538 Å °-0.0889 Å °0.0657 Å °0.0317 Å °
Refinement TLS groupSelection details: all

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