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- PDB-7v8q: Crystal structure of antibody 14A in complex with MUC1 Glycopepti... -

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Basic information

Entry
Database: PDB / ID: 7v8q
TitleCrystal structure of antibody 14A in complex with MUC1 Glycopeptide(GlycoT)
Components
  • 14A fab heavy chain
  • 14A fab light chain
  • Mucin-1 subunit alpha
KeywordsIMMUNE SYSTEM / Antibody / anti-MUC1 / Cancer / 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: 3.2 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 23, 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
Revision 1.2Nov 20, 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)148,55812
Polymers147,8949
Non-polymers6643
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)49,5194
Polymers49,2983
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-33 kcal/mol
Surface area19390 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)49,5194
Polymers49,2983
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-33 kcal/mol
Surface area19250 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)49,5194
Polymers49,2983
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-30 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.890, 207.373, 224.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32
13
23
33

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
111GLNGLNARGARG(chain 'A' and resid 1 through 215)AA1 - 2141 - 214
211GLNGLNARGARG(chain 'C' and resid 1 through 215)CC1 - 2141 - 214
311GLNGLNARGARGchain 'E'EE1 - 2141 - 214
112GLUGLUALAALA(chain 'B' and (resid 2 through 132 or resid 135 through 218))BB2 - 1292 - 129
122THRTHRPROPRO(chain 'B' and (resid 2 through 132 or resid 135 through 218))BB135 - 217135 - 217
212GLUGLUALAALA(chain 'D' and (resid 2 through 131 or resid 135 through 218))DD2 - 1292 - 129
222THRTHRPROPRO(chain 'D' and (resid 2 through 131 or resid 135 through 218))DD135 - 217135 - 217
312GLUGLUALAALA(chain 'F' and resid 2 through 218)FF2 - 1292 - 129
322THRTHRPROPRO(chain 'F' and resid 2 through 218)FF135 - 217135 - 217
113SERSERHISHISchain 'G'GG6 - 126 - 12
123NGANGANGANGAchain 'G'GJ101
213SERSERHISHIS(chain 'H' and resid 6 through 101)HH6 - 126 - 12
223NGANGANGANGA(chain 'H' and resid 6 through 101)HK101
313SERSERHISHISchain 'I'II6 - 126 - 12
323NGANGANGANGAchain 'I'IL101

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.: 3
Source method: isolated from a genetically manipulated 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
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: 63.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Crystal screen D4=JCSG F7, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 20% v/v 2-Propanol, 20% w/v Polyethylene glycol 4000

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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: 3.2→39.63 Å / Num. obs: 33766 / % possible obs: 98.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 72.24 Å2 / CC1/2: 0.989 / Rpim(I) all: 0.091 / Rrim(I) all: 0.315 / Net I/σ(I): 5
Reflection shellResolution: 3.2→3.32 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 3260 / CC1/2: 0.766 / Rpim(I) all: 0.249 / Rrim(I) all: 0.754

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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: 3.2→39.63 Å / SU ML: 0.4128 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.6692
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2442 1669 4.95 %
Rwork0.2004 32055 -
obs0.2026 33724 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.37 Å2
Refinement stepCycle: LAST / Resolution: 3.2→39.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10028 0 0 0 10028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004310257
X-RAY DIFFRACTIONf_angle_d0.859613971
X-RAY DIFFRACTIONf_chiral_restr0.05041613
X-RAY DIFFRACTIONf_plane_restr0.00511770
X-RAY DIFFRACTIONf_dihedral_angle_d15.73281426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.30.33631400.29142583X-RAY DIFFRACTION95.61
3.3-3.410.33531320.28532568X-RAY DIFFRACTION98.76
3.41-3.530.33951480.25822646X-RAY DIFFRACTION98.87
3.53-3.670.30171250.25092622X-RAY DIFFRACTION99.67
3.67-3.840.33681180.24762697X-RAY DIFFRACTION99.51
3.84-4.040.25331470.22652649X-RAY DIFFRACTION99.75
4.04-4.290.22181510.18352727X-RAY DIFFRACTION99.69
4.29-4.620.20091260.15982652X-RAY DIFFRACTION99.61
4.62-5.080.19061460.15112694X-RAY DIFFRACTION99.68
5.08-5.820.21021630.17772677X-RAY DIFFRACTION98.95
5.82-7.320.27421460.19382765X-RAY DIFFRACTION98.68
7.32-39.630.19081270.17592775X-RAY DIFFRACTION93.86

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