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- PDB-7v3q: Crystal structure of anti-MUC1 antibody 16A -

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Basic information

Entry
Database: PDB / ID: 7v3q
TitleCrystal structure of anti-MUC1 antibody 16A
Components
  • Fab 16A Heavy Chain
  • Fab 16A Light Chain
KeywordsIMMUNE SYSTEM / Antibody / anti-MUC1 / Cancer / ANTITUMOR PROTEIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.98 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 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 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 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fab 16A Light Chain
B: Fab 16A Heavy Chain
C: Fab 16A Light Chain
D: Fab 16A Heavy Chain


Theoretical massNumber of molelcules
Total (without water)95,0594
Polymers95,0594
Non-polymers00
Water00
1
A: Fab 16A Light Chain
B: Fab 16A Heavy Chain


Theoretical massNumber of molelcules
Total (without water)47,5292
Polymers47,5292
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-28 kcal/mol
Surface area18900 Å2
MethodPISA
2
C: Fab 16A Light Chain
D: Fab 16A Heavy Chain


Theoretical massNumber of molelcules
Total (without water)47,5292
Polymers47,5292
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-26 kcal/mol
Surface area18870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.632, 126.696, 158.201
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
12
22

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
111ALAALAARGARGchain 'A'AA2 - 2142 - 214
211ALAALAARGARG(chain 'C' and resid 2 through 215)CC2 - 2142 - 214
122GLUGLUGLUGLU(chain 'B' and resid 2 through 217)BB2 - 2162 - 216
222GLUGLUGLUGLUchain 'D'DD2 - 2162 - 216

NCS ensembles :
ID
1
2

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Components

#1: Antibody Fab 16A Light Chain


Mass: 23543.229 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichopalpus nigribasis (fry)
#2: Antibody Fab 16A Heavy Chain


Mass: 23986.049 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichopalpus nigribasis (fry)
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: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.0 M Lithium chloride 0.1 M Tris pH 8.5 20%(w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.98→48.68 Å / Num. obs: 18236 / % possible obs: 97.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 42.91 Å2 / CC1/2: 0.97 / Rpim(I) all: 0.086 / Rrim(I) all: 0.184 / Net I/σ(I): 9.1
Reflection shellResolution: 2.98→3.09 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1686 / CC1/2: 0.707 / Rpim(I) all: 0.35 / Rrim(I) all: 0.728 / % possible all: 92.3

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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: 2.98→48.68 Å / SU ML: 0.2622 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.0908
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2637 888 4.87 %
Rwork0.2181 17335 -
obs0.2203 18223 97.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.69 Å2
Refinement stepCycle: LAST / Resolution: 2.98→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6556 0 0 0 6556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00456710
X-RAY DIFFRACTIONf_angle_d0.83759136
X-RAY DIFFRACTIONf_chiral_restr0.05961045
X-RAY DIFFRACTIONf_plane_restr0.00551161
X-RAY DIFFRACTIONf_dihedral_angle_d16.8705917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.98-3.170.31711430.27132732X-RAY DIFFRACTION94.67
3.17-3.420.31671530.26462845X-RAY DIFFRACTION98.65
3.42-3.760.27491360.22842878X-RAY DIFFRACTION98.66
3.76-4.30.28471520.21462926X-RAY DIFFRACTION99.13
4.3-5.420.21221520.17792907X-RAY DIFFRACTION98.36
5.42-48.680.23651520.20723047X-RAY DIFFRACTION97.23
Refinement TLS params.Method: refined / Origin x: 56.2554536026 Å / Origin y: 36.6470574259 Å / Origin z: 195.849289822 Å
111213212223313233
T0.123442828377 Å20.0043239586765 Å2-0.0477807963506 Å2-0.229884195223 Å2-0.00373370985555 Å2--0.228444796441 Å2
L0.363819031168 °20.0203741241957 °2-0.335697949722 °2-0.378658333721 °20.22671391387 °2--0.727665772231 °2
S0.0301111232776 Å °-0.0140534276681 Å °-0.0286788206009 Å °-0.0251703125821 Å °-0.00955939969687 Å °-0.0227554021764 Å °-0.0238000232653 Å °0.0145152528115 Å °-0.0178675455739 Å °
Refinement TLS groupSelection details: all

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