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

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Basic information

Entry
Database: PDB / ID: 7vaz
TitleCrystal structure of antibody 14A in complex with MUC1 glycopeptide(GlycoS)
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 / DNA damage response, signal transduction by p53 class mediator ...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 / DNA damage response, signal transduction by p53 class mediator / localization / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / transcription coregulator activity / 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
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: 2.73 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 30, 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 ...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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 14A fab light chain
D: 14A fab heavy chain
G: Mucin-1 subunit alpha
A: 14A fab light chain
B: 14A fab heavy chain
E: Mucin-1 subunit alpha
F: 14A fab light chain
H: 14A fab heavy chain
I: Mucin-1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,11610
Polymers147,8949
Non-polymers2211
Water1086
1
C: 14A fab light chain
D: 14A fab heavy chain
G: Mucin-1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5194
Polymers49,2983
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 14A fab light chain
B: 14A fab heavy chain
E: Mucin-1 subunit alpha


Theoretical massNumber of molelcules
Total (without water)49,2983
Polymers49,2983
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: 14A fab light chain
H: 14A fab heavy chain
I: Mucin-1 subunit alpha


Theoretical massNumber of molelcules
Total (without water)49,2983
Polymers49,2983
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.558, 226.620, 71.071
Angle α, β, γ (deg.)90.000, 107.690, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 144 or resid 146 through 214))
21(chain C and (resid 2 through 144 or resid 146 through 214))
31(chain F and (resid 2 through 144 or resid 146 through 214))
12(chain B and (resid 3 through 128 or resid 135 through 214))
22(chain D and (resid 3 through 128 or resid 135 through 214))
32(chain H and (resid 3 through 128 or resid 135 through 214))
13chain E
23(chain G and resid 4 through 13)

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
111ALAALAPROPRO(chain A and (resid 2 through 144 or resid 146 through 214))AD2 - 1442 - 144
121GLUGLUARGARG(chain A and (resid 2 through 144 or resid 146 through 214))AD146 - 214146 - 214
211ALAALAPROPRO(chain C and (resid 2 through 144 or resid 146 through 214))CA2 - 1442 - 144
221GLUGLUARGARG(chain C and (resid 2 through 144 or resid 146 through 214))CA146 - 214146 - 214
311ALAALAPROPRO(chain F and (resid 2 through 144 or resid 146 through 214))FG2 - 1442 - 144
321GLUGLUARGARG(chain F and (resid 2 through 144 or resid 146 through 214))FG146 - 214146 - 214
112VALVALLEULEU(chain B and (resid 3 through 128 or resid 135 through 214))BE3 - 1283 - 128
122THRTHRLYSLYS(chain B and (resid 3 through 128 or resid 135 through 214))BE135 - 214135 - 214
212VALVALLEULEU(chain D and (resid 3 through 128 or resid 135 through 214))DB3 - 1283 - 128
222THRTHRLYSLYS(chain D and (resid 3 through 128 or resid 135 through 214))DB135 - 214135 - 214
312VALVALLEULEU(chain H and (resid 3 through 128 or resid 135 through 214))HH3 - 1283 - 128
322THRTHRLYSLYS(chain H and (resid 3 through 128 or resid 135 through 214))HH135 - 214135 - 214
113PROPROGLYGLYchain EEF4 - 134 - 13
213PROPROGLYGLY(chain G and resid 4 through 13)GC4 - 134 - 13

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 / N-Acetylgalactosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: isolated from a natural source / 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.41 Å3/Da / Density % sol: 49 %
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: Dec 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.73→44.36 Å / Num. obs: 36287 / % possible obs: 98.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 41.78 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.05 / Rrim(I) all: 0.131 / Net I/σ(I): 10.8
Reflection shellResolution: 2.73→2.83 Å / Num. unique obs: 3078 / CC1/2: 0.846 / Rpim(I) all: 0.208 / Rrim(I) all: 0.485

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Processing

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

4yhy


Resolution: 2.73→44.36 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 27.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2635 2005 5.53 %
Rwork0.2094 34272 -
obs0.2124 36277 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.73 Å2 / Biso mean: 42.8099 Å2 / Biso min: 13.97 Å2
Refinement stepCycle: final / Resolution: 2.73→44.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9864 0 28 6 9898
Biso mean--39.27 22.3 -
Num. residues----1306
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1908X-RAY DIFFRACTION7.938TORSIONAL
12C1908X-RAY DIFFRACTION7.938TORSIONAL
13F1908X-RAY DIFFRACTION7.938TORSIONAL
21B1848X-RAY DIFFRACTION7.938TORSIONAL
22D1848X-RAY DIFFRACTION7.938TORSIONAL
23H1848X-RAY DIFFRACTION7.938TORSIONAL
31E54X-RAY DIFFRACTION7.938TORSIONAL
32G54X-RAY DIFFRACTION7.938TORSIONAL
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 (%)
2.73-2.80.38961160.29121911202779
2.8-2.880.32181420.26672485262799
2.88-2.960.27881510.253124852636100
2.96-3.060.31371480.252224452593100
3.06-3.170.3411400.251125102650100
3.17-3.30.30411540.236624812635100
3.3-3.450.2851440.235624692613100
3.45-3.630.29661410.220824872628100
3.63-3.850.30591460.217625052651100
3.85-4.150.26191460.197924842630100
4.15-4.570.2271380.16524912629100
4.57-5.230.20611440.162825102654100
5.23-6.580.20711500.195725042654100
6.59-44.360.22431450.194225052650100
Refinement TLS params.Method: refined / Origin x: 1.4401 Å / Origin y: 38.787 Å / Origin z: 10.0494 Å
111213212223313233
T0.1044 Å2-0.0038 Å20.0015 Å2-0.238 Å20.0056 Å2--0.1879 Å2
L0.2507 °2-0.0243 °20.0286 °2-0.8109 °20.1 °2--0.4659 °2
S0.0077 Å °-0.025 Å °0.0173 Å °-0.0014 Å °-0.0336 Å °-0.1017 Å °-0.0162 Å °-0.0651 Å °0.0219 Å °
Refinement TLS groupSelection details: all

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