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- PDB-3r06: Crystal structure of anti-mouse CD3epsilon antibody 2C11 Fab fragment -

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Basic information

Entry
Database: PDB / ID: 3r06
TitleCrystal structure of anti-mouse CD3epsilon antibody 2C11 Fab fragment
Components
  • anti-mouse CD3epsilon antibody 2C11 Fab heavy chain
  • anti-mouse CD3epsilon antibody 2C11 Fab light chain
KeywordsIMMUNE SYSTEM / antibody / anti-CD3epsilon / T-cell receptor / signalling
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesCricetulus migratorius (Armenian hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsShore, D.A. / Zhu, X. / Wilson, I.A.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: T cell receptors are structures capable of initiating signaling in the absence of large conformational rearrangements.
Authors: Fernandes, R.A. / Shore, D.A. / Vuong, M.T. / Yu, C. / Zhu, X. / Pereira-Lopes, S. / Brouwer, H. / Fennelly, J.A. / Jessup, C.M. / Evans, E.J. / Wilson, I.A. / Davis, S.J.
History
DepositionMar 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: anti-mouse CD3epsilon antibody 2C11 Fab light chain
B: anti-mouse CD3epsilon antibody 2C11 Fab heavy chain
C: anti-mouse CD3epsilon antibody 2C11 Fab light chain
D: anti-mouse CD3epsilon antibody 2C11 Fab heavy chain
E: anti-mouse CD3epsilon antibody 2C11 Fab light chain
F: anti-mouse CD3epsilon antibody 2C11 Fab heavy chain
H: anti-mouse CD3epsilon antibody 2C11 Fab heavy chain
L: anti-mouse CD3epsilon antibody 2C11 Fab light chain


Theoretical massNumber of molelcules
Total (without water)187,1818
Polymers187,1818
Non-polymers00
Water7,368409
1
A: anti-mouse CD3epsilon antibody 2C11 Fab light chain
B: anti-mouse CD3epsilon antibody 2C11 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)46,7952
Polymers46,7952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-22 kcal/mol
Surface area19530 Å2
MethodPISA
2
C: anti-mouse CD3epsilon antibody 2C11 Fab light chain
D: anti-mouse CD3epsilon antibody 2C11 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)46,7952
Polymers46,7952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-25 kcal/mol
Surface area19900 Å2
MethodPISA
3
E: anti-mouse CD3epsilon antibody 2C11 Fab light chain
F: anti-mouse CD3epsilon antibody 2C11 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)46,7952
Polymers46,7952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-24 kcal/mol
Surface area19930 Å2
MethodPISA
4
H: anti-mouse CD3epsilon antibody 2C11 Fab heavy chain
L: anti-mouse CD3epsilon antibody 2C11 Fab light chain


Theoretical massNumber of molelcules
Total (without water)46,7952
Polymers46,7952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-26 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.171, 72.386, 127.487
Angle α, β, γ (deg.)90.00, 109.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
anti-mouse CD3epsilon antibody 2C11 Fab light chain


Mass: 23646.154 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus migratorius (Armenian hamster)
Cell: hybridoma
#2: Antibody
anti-mouse CD3epsilon antibody 2C11 Fab heavy chain


Mass: 23149.064 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus migratorius (Armenian hamster)
Cell: hybridoma
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5
Details: 0.1M HEPES, PEG 4000, pH 7.5, EVAPORATION, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1
DetectorDetector: ADSC QUANTUM 315 / Date: Jun 19, 2006
RadiationMonochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 62077 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 62.61 Å2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 90.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.5→36.02 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.909 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3142 5.06 %RANDOM
Rwork0.191 ---
obs0.193 62054 --
Displacement parametersBiso max: 166.5 Å2 / Biso mean: 60.4514 Å2 / Biso min: 24.2 Å2
Baniso -1Baniso -2Baniso -3
1--8.6931 Å20 Å25.448 Å2
2--9.8123 Å20 Å2
3----1.1192 Å2
Refine analyzeLuzzati coordinate error obs: 0.347 Å
Refinement stepCycle: LAST / Resolution: 2.5→36.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13018 0 0 409 13427
Refine LS restraints
Refine-IDTypeNumberWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d44062
X-RAY DIFFRACTIONt_trig_c_planes2922
X-RAY DIFFRACTIONt_gen_planes19275
X-RAY DIFFRACTIONt_it1333820
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion17955
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact145264
X-RAY DIFFRACTIONt_bond_d1333820.01
X-RAY DIFFRACTIONt_angle_deg1817221.22
X-RAY DIFFRACTIONt_omega_torsion3.36
X-RAY DIFFRACTIONt_other_torsion19.82
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2525 211 5.71 %
Rwork0.2242 3486 -
all0.2259 3697 -
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)
15.09013.54482.40944.64742.52944.16260.15360.3325-0.45960.1059-0.0267-0.00990.6967-0.0378-0.12680.06290.00520.0179-0.1787-0.0541-0.1293-1.529815.1582-31.5288
22.6623-0.6381-1.10551.7139-0.40982.2270.0012-0.27410.01760.25440.09520.14920.0679-0.0291-0.09630.0488-0.0196-0.0257-0.120.0037-0.11081.408322.33223.3415
31.38611.59340.19951.96050.961511.2468-0.0143-0.3209-0.1031-0.1007-0.12220.37880.3981-0.15770.13650.0361-0.0213-0.0443-0.1218-0.056-0.1718-23.516110.6345-26.7317
42.1021.52210.12282.63920.43061.3823-0.1215-0.0716-0.04540.13490.08640.08080.0233-0.07050.03510.03930.0299-0.0392-0.13290.0345-0.0448-10.825131.6587-1.1663
53.23141.03690.21360.8034-1.05145.16880.01480.00770.36960.0735-0.07240.057-0.6872-0.37960.05770.00980.0891-0.0354-0.1755-0.0459-0.05448.910210.391336.7933
62.8944-0.23711.40962.18460.60442.65720.0240.09340.16760.37880.0113-0.17540.04760.1087-0.03530.1776-0.0216-0.0969-0.2466-0.0204-0.110332.9053.15963.3434
74.97480.79082.66552.0584-0.51774.2531-0.1730.88350.4126-0.0232-0.0238-0.1782-0.30070.35020.1968-0.0344-0.0014-0.046-0.06550.0611-0.093426.252811.384121.6934
81.4850.3657-0.20161.5607-1.52382.90440.04740.10810.07220.26850.0623-0.10760.00410.0768-0.10970.20050.0176-0.0663-0.2481-0.0383-0.094138.115-6.121751.3857
92.8687-0.35240.54553.79743.23493.1755-0.1019-0.06950.45560.04320.02160.2426-0.45350.1940.0803-0.0475-0.03910.0762-0.1503-0.00960.022578.1837-8.741718.8125
104.59990.86210.64762.1126-0.5252.3168-0.11120.11420.3179-0.31210.09410.25870.0077-0.30240.01710.05680.0016-0.0808-0.15380.0196-0.130751.4039-17.1506-3.3616
115.2787-0.57491.54633.47920.69633.93470.07420.29740.19170.09090.1571-0.3008-0.1280.0269-0.2314-0.10690.00730.0159-0.09380.0134-0.092762.0093-4.221134.2508
121.58760.1627-0.18883.28472.50623.24570.1149-0.1114-0.0577-0.0611-0.08510.02560.1587-0.2506-0.02980.0835-0.0135-0.1014-0.11970.0151-0.097448.105-26.16629.3505
132.2091-0.89290.66191.0173-0.31632.64680.2204-0.1503-0.6203-0.0058-0.05770.17390.2644-0.0656-0.16280.1918-0.0686-0.0833-0.2270.0484-0.0728-15.8467-3.926592.3249
142.27810.4647-0.64672.49511.14053.5724-0.01340.09650.0267-0.21190.09560.0757-0.06380.054-0.08220.09680.0374-0.0831-0.19760.0011-0.1031-23.5343.576357.3783
154.1542-0.2631-0.00672.6250.61526.2604-0.0107-0.3795-0.1916-0.3082-0.152-0.11360.24920.42310.16270.10120.0374-0.006-0.20720.079-0.17836.3367-5.49786.2759
161.7188-2.37680.37223.9469-0.68671.34210.02040.12140.1751-0.031-0.0581-0.19580.05960.03080.03770.1168-0.0245-0.0845-0.1932-0.0169-0.0407-10.671212.790960.1577
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth seq-ID
1X-RAY DIFFRACTION1A 1 A 1100
2X-RAY DIFFRACTION2A 111 A 2130
3X-RAY DIFFRACTION3B 1 B 1100
4X-RAY DIFFRACTION4B 111 B 2160
5X-RAY DIFFRACTION5C 1 C 1100
6X-RAY DIFFRACTION6C 111 C 2130
7X-RAY DIFFRACTION7D 1 D 1100
8X-RAY DIFFRACTION8D 111 D 2160
9X-RAY DIFFRACTION9E 1 E 1100
10X-RAY DIFFRACTION10E 111 E 2130
11X-RAY DIFFRACTION11F 1 F 1100
12X-RAY DIFFRACTION12F 111 F 2160
13X-RAY DIFFRACTION13L 1 L 1100
14X-RAY DIFFRACTION14L 111 L 2130
15X-RAY DIFFRACTION15H 1 H 1100
16X-RAY DIFFRACTION16H 111 H 2160

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