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- PDB-7re9: TCR mimic antibody (Fab fragment) -

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Basic information

Entry
Database: PDB / ID: 7re9
TitleTCR mimic antibody (Fab fragment)
Components
  • Fab heavy chain
  • Fab light chain
KeywordsIMMUNE SYSTEM / TCR mimic antibody (Fab fragment)
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsDasgupta, M. / Baker, B.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Sci Rep / Year: 2022
Title: Validation and promise of a TCR mimic antibody for cancer immunotherapy of hepatocellular carcinoma.
Authors: Liu, C. / Liu, H. / Dasgupta, M. / Hellman, L.M. / Zhang, X. / Qu, K. / Xue, H. / Wang, Y. / Fan, F. / Chang, Q. / Yu, D. / Ge, L. / Zhang, Y. / Cui, Z. / Zhang, P. / Heller, B. / Zhang, H. ...Authors: Liu, C. / Liu, H. / Dasgupta, M. / Hellman, L.M. / Zhang, X. / Qu, K. / Xue, H. / Wang, Y. / Fan, F. / Chang, Q. / Yu, D. / Ge, L. / Zhang, Y. / Cui, Z. / Zhang, P. / Heller, B. / Zhang, H. / Shi, B. / Baker, B.M. / Liu, C.
History
DepositionJul 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
H: Fab heavy chain
L: Fab light chain
A: Fab heavy chain
B: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1056
Polymers93,8924
Non-polymers2122
Water97354
1
H: Fab heavy chain
L: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1584
Polymers46,9462
Non-polymers2122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-19 kcal/mol
Surface area18960 Å2
MethodPISA
2
A: Fab heavy chain
B: Fab light chain


Theoretical massNumber of molelcules
Total (without water)46,9462
Polymers46,9462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-20 kcal/mol
Surface area19300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.325, 40.348, 161.807
Angle α, β, γ (deg.)90.000, 105.150, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 131 or resid 139 through 217))
21(chain H and (resid 2 through 131 or resid 139 through 217))
12(chain B and resid 3 through 212)
22(chain L and resid 3 through 212)

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
111VALVALSERSER(chain A and (resid 2 through 131 or resid 139 through 217))AC2 - 1312 - 131
121THRTHRPROPRO(chain A and (resid 2 through 131 or resid 139 through 217))AC139 - 217139 - 217
211VALVALSERSER(chain H and (resid 2 through 131 or resid 139 through 217))HA2 - 1312 - 131
221THRTHRPROPRO(chain H and (resid 2 through 131 or resid 139 through 217))HA139 - 217139 - 217
112VALVALPROPRO(chain B and resid 3 through 212)BD3 - 2123 - 212
212VALVALPROPRO(chain L and resid 3 through 212)LB3 - 2123 - 212

NCS ensembles :
ID
1
2

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Components

#1: Antibody Fab heavy chain


Mass: 24068.963 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab light chain


Mass: 22877.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop
Details: 15% w/v Polyethylene glycol 6,000 and 5.00 % w/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.77→66.35 Å / Num. obs: 21759 / % possible obs: 99.1 % / Redundancy: 6.3 % / CC1/2: 0.967 / Net I/σ(I): 8.9
Reflection shellResolution: 2.77→2.82 Å / Num. unique obs: 1118 / CC1/2: 0.516

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
PHENIXmodel building
DIALSdata scaling
PHASERphasing
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M6M, 6PZH

4m6m

6pzh


Resolution: 2.77→66.33 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2674 2147 9.99 %
Rwork0.2231 19336 -
obs0.2275 21483 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.25 Å2 / Biso mean: 33.3405 Å2 / Biso min: 0.99 Å2
Refinement stepCycle: final / Resolution: 2.77→66.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6309 0 14 54 6377
Biso mean--46.75 11.79 -
Num. residues----840
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1849X-RAY DIFFRACTION9.685TORSIONAL
12H1849X-RAY DIFFRACTION9.685TORSIONAL
21B1881X-RAY DIFFRACTION9.685TORSIONAL
22L1881X-RAY DIFFRACTION9.685TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.77-2.830.42281440.31291278142297
2.83-2.910.37141360.29461250138695
2.91-2.980.33171380.28781222136097
2.98-3.070.31341420.2861286142896
3.07-3.170.32081380.26361256139498
3.17-3.280.31041410.26641260140197
3.28-3.420.33621430.26341276141998
3.42-3.570.25661380.22811268140697
3.57-3.760.29461460.22381308145499
3.76-3.990.25121440.19211297144199
4-4.30.20781470.187313211468100
4.3-4.740.16881450.15581298144399
4.74-5.420.18451450.1581314145999
5.42-6.830.26121470.21111322146997
6.83-66.330.27241530.22231380153398
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.865-1.3844-1.14993.58521.04642.57050.02280.64270.4793-0.6325-0.58170.4173-0.7057-0.6443-0.6230.24040.0735-0.05080.1449-0.0730.31010.43815.08857.5875
22.44490.8217-0.76752.39290.09682.39240.0836-0.1545-0.0075-0.0656-0.04490.04440.26950.0367-0.03670.199-0.0161-0.03340.1891-0.0360.182818.869-5.618247.7261
36.2651.38180.37951.2702-0.54671.45840.2213-0.5191-1.39320.3476-0.1891-0.76110.4914-0.3612-0.11620.3635-0.11190.02240.245-0.02750.274620.8382-14.302853.0834
41.6268-1.40390.12831.5841-0.40631.32140.1279-0.1190.0608-0.0627-0.02210.0010.0038-0.0043-0.03440.2292-0.0236-0.00740.2005-0.02110.216851.5094-5.797546.8441
53.2578-0.21722.03012.534-1.11492.72330.039-0.17840.10470.0434-0.05810.19720.4809-0.26260.0760.2531-0.10220.01130.3333-0.0350.225923.0884-15.46369.0355
63.20691.4718-1.57062.7334-2.24612.714-0.0001-0.04070.14330.2226-0.02790.0799-0.25540.0670.05230.2537-0.0463-0.0010.2568-0.00850.180358.1145-2.053362.0681
72.2951-1.59620.66171.1154-0.48170.5064-0.00410.0037-0.0088-0.03880.16330.41810.36350.58540.12770.37270.07790.04280.1359-0.02810.306833.0838-11.037732.1222
80.30280.38970.02072.03030.26771.5679-0.1324-0.0089-0.17760.41830.11680.0447-0.14050.12890.03590.27260.00820.01980.12690.04660.282439.772-13.408328.1439
92.83311.15180.95251.2051-1.51245.48960.12430.5118-0.7166-0.2937-0.234-0.33350.18060.7842-0.34350.2936-0.0267-0.06840.2229-0.0590.273148.4518-16.246524.6009
101.99330.0334-0.40494.749-1.02914.46610.31930.3750.0956-0.61610.1711-0.57160.02260.86280.71550.1778-0.0744-0.11310.2060.1420.175147.3502-11.384628.5905
111.44320.51960.18692.6899-0.50771.76520.08780.328-0.1424-0.2061-0.1795-0.1592-0.08480.17680.09090.15950.0097-0.00280.143-0.02450.243138.6714-11.853625.5765
120.6248-0.5042-1.81862.70641.39445.50380.3033-0.34040.79380.198-0.77210.44740.1126-1.3818-0.79540.4497-0.1489-0.0537-0.28870.09040.2411.87385.245326.6089
131.56640.4526-0.28141.19160.10991.9426-0.2599-0.0743-0.0044-0.50450.1167-0.07050.2804-0.3301-0.01370.22350.0188-0.04630.217-0.01370.37213.4208-1.007424.9919
142.7173-2.6661-0.03262.65670.2312.4979-1.0285-0.3301-0.7365-0.25960.08460.75640.2491-1.0461-0.18880.3593-0.1096-0.00490.5385-0.15520.3186-1.1048-6.304628.4261
152.13251.38381.01520.88250.70732.30070.3707-0.2361-0.62940.1091-0.0171-0.49050.3766-0.39010.37460.1395-0.0216-0.0090.2805-0.00120.324716.2931-0.632333.6057
164.05381.12070.31693.0712-0.58750.30240.4259-0.54760.54750.0136-0.50410.6126-0.25020.19510.05410.40540.10070.09930.4183-0.10730.29857.63571.7334.9635
172.08410.05470.70432.9251-0.14893.6918-0.15910.3761-0.0806-0.0980.1902-0.1092-0.14640.3842-0.07850.2509-0.06230.03330.2384-0.10850.281434.5036-23.87628.922
182.33440.1048-0.75721.0081-0.42060.9365-0.1312-0.28150.1280.07350.18460.2792-0.2468-0.0608-0.00540.49770.114-0.05430.2421-0.03580.35434.94041.654916.5478
192.84110.6877-0.24662.39221.07263.7854-0.0562-0.0790.17740.0550.1702-0.0631-0.04350.12510.01690.19360.0511-0.0420.25230.00910.268.49493.580211.688
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'L' and (resid 192 through 212 )L192 - 212
2X-RAY DIFFRACTION2chain 'A' and (resid 2 through 91 )A2 - 91
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 110 )A92 - 110
4X-RAY DIFFRACTION4chain 'A' and (resid 111 through 217 )A111 - 217
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 109 )B3 - 109
6X-RAY DIFFRACTION6chain 'B' and (resid 110 through 213 )B110 - 213
7X-RAY DIFFRACTION7chain 'H' and (resid 2 through 12 )H2 - 12
8X-RAY DIFFRACTION8chain 'H' and (resid 13 through 44 )H13 - 44
9X-RAY DIFFRACTION9chain 'H' and (resid 45 through 60 )H45 - 60
10X-RAY DIFFRACTION10chain 'H' and (resid 61 through 77 )H61 - 77
11X-RAY DIFFRACTION11chain 'H' and (resid 78 through 115 )H78 - 115
12X-RAY DIFFRACTION12chain 'H' and (resid 116 through 139 )H116 - 139
13X-RAY DIFFRACTION13chain 'H' and (resid 140 through 181 )H140 - 181
14X-RAY DIFFRACTION14chain 'H' and (resid 182 through 198 )H182 - 198
15X-RAY DIFFRACTION15chain 'H' and (resid 199 through 207 )H199 - 207
16X-RAY DIFFRACTION16chain 'H' and (resid 208 through 217 )H208 - 217
17X-RAY DIFFRACTION17chain 'L' and (resid 3 through 109 )L3 - 109
18X-RAY DIFFRACTION18chain 'L' and (resid 110 through 133 )L110 - 133
19X-RAY DIFFRACTION19chain 'L' and (resid 134 through 191 )L134 - 191

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