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- PDB-3bky: Crystal Structure of Chimeric Antibody C2H7 Fab in complex with a... -

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Basic information

Entry
Database: PDB / ID: 3bky
TitleCrystal Structure of Chimeric Antibody C2H7 Fab in complex with a CD20 Peptide
Components
  • B-lymphocyte antigen CD20
  • the Fab fragment of chimeric 2H7, heavy chain
  • the Fab fragment of chimeric 2H7, light chain
KeywordsIMMUNE SYSTEM / 2H7 / C2H7 / chimeric antibody / Fab / CD20 / Fab-peptide complex / B-cell activation / Membrane / Phosphoprotein / Transmembrane
Function / homology
Function and homology information


store-operated calcium entry / positive regulation of calcium ion import across plasma membrane / calcium ion import into cytosol / epidermal growth factor receptor binding / B cell activation / B cell proliferation / plasma membrane raft / immunoglobulin binding / humoral immune response / B cell differentiation ...store-operated calcium entry / positive regulation of calcium ion import across plasma membrane / calcium ion import into cytosol / epidermal growth factor receptor binding / B cell activation / B cell proliferation / plasma membrane raft / immunoglobulin binding / humoral immune response / B cell differentiation / response to bacterium / protein tetramerization / B cell receptor signaling pathway / MHC class II protein complex binding / cell surface receptor signaling pathway / external side of plasma membrane / cell surface / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / plasma membrane
Similarity search - Function
CD20-like family / Membrane-spanning 4-domains subfamily A / CD20-like family / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
B-lymphocyte antigen CD20
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.61 Å
AuthorsDu, J. / Zhong, C. / Ding, J.
CitationJournal: Mol.Immunol. / Year: 2008
Title: Crystal structure of chimeric antibody C2H7 Fab in complex with a CD20 peptide
Authors: Du, J. / Wang, H. / Zhong, C. / Peng, B. / Zhang, M. / Li, B. / Hou, S. / Guo, Y. / Ding, J.
History
DepositionDec 7, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jan 29, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct_ref
Item: _entity.details / _entity_src_gen.gene_src_common_name ..._entity.details / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_ref.pdbx_seq_one_letter_code
Revision 1.4Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 10, 2024Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.gene_src_genus

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: the Fab fragment of chimeric 2H7, heavy chain
L: the Fab fragment of chimeric 2H7, light chain
P: B-lymphocyte antigen CD20


Theoretical massNumber of molelcules
Total (without water)50,2133
Polymers50,2133
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: the Fab fragment of chimeric 2H7, heavy chain
L: the Fab fragment of chimeric 2H7, light chain


Theoretical massNumber of molelcules
Total (without water)47,3612
Polymers47,3612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-29 kcal/mol
Surface area19700 Å2
MethodPISA
3
P: B-lymphocyte antigen CD20


Theoretical massNumber of molelcules
Total (without water)2,8521
Polymers2,8521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.490, 96.490, 107.613
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Antibody the Fab fragment of chimeric 2H7, heavy chain


Mass: 24220.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: chimeric 2H7, heavy chain from Human and Mouse / Source: (gene. exp.) Homo sapiens (human) / Species: , / Plasmid: pcDNA3.1 / Cell line (production host): Chinese hamster ovary (CHO) / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): K1
#2: Antibody the Fab fragment of chimeric 2H7, light chain


Mass: 23140.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: chimeric 2H7, light chain from Human and Mouse / Source: (gene. exp.) Homo sapiens (human) / Species: , / Plasmid: pcDNA3.1 / Cell line (production host): Chinese hamster ovary (CHO) / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): K1
#3: Protein/peptide B-lymphocyte antigen CD20 / B-lymphocyte surface antigen B1 / Bp35 / Leukocyte surface antigen Leu-16 / Membrane-spanning 4- ...B-lymphocyte surface antigen B1 / Bp35 / Leukocyte surface antigen Leu-16 / Membrane-spanning 4-domains subfamily A member 1


Mass: 2852.051 Da / Num. of mol.: 1 / Fragment: CD20 peptide, resideus 163-187 / Source method: obtained synthetically
Details: the CD20 peptide was synthesized at Shanghai HB Bioscience Company
Source: (synth.) Homo sapiens (human) / References: UniProt: P11836
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 0.2M di-ammonium hydrogen phosphate, 20% PEG3350, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 16029 / Num. obs: 15644 / % possible obs: 97.6 % / Redundancy: 11.4 % / Biso Wilson estimate: 61.2 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Χ2: 1.183 / Net I/σ(I): 8.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 4.5 / Num. unique all: 1538 / Rsym value: 0.488 / Χ2: 0.945 / % possible all: 98.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OSL

2osl


Resolution: 2.61→20 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.873 / SU B: 31.771 / SU ML: 0.335 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.617 / ESU R Free: 0.396 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.301 781 5 %RANDOM
Rwork0.234 ---
obs0.237 15609 97.7 %-
all-15976 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å20 Å2
2---0.93 Å20 Å2
3---1.86 Å2
Refinement stepCycle: LAST / Resolution: 2.61→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3456 0 0 117 3573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223551
X-RAY DIFFRACTIONr_angle_refined_deg1.221.9484841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4955453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.17624.586133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.23615554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.546159
X-RAY DIFFRACTIONr_chiral_restr0.0860.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022677
X-RAY DIFFRACTIONr_nbd_refined0.2230.21690
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22340
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2174
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2680.210
X-RAY DIFFRACTIONr_mcbond_it0.3481.52323
X-RAY DIFFRACTIONr_mcangle_it0.59523685
X-RAY DIFFRACTIONr_scbond_it0.72631428
X-RAY DIFFRACTIONr_scangle_it1.1794.51156
LS refinement shellResolution: 2.61→2.677 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.485 59 -
Rwork0.359 1098 -
all-1157 -
obs--98.72 %
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)
112.18748.17739.97085.74564.109433.86960.13960.7321-0.3480.42922.0353-1.6712.08872.7952-2.17480.42280.47540.29220.57620.16770.618822.0001-16.9844-10.9895
212.50042.40160.27550.67810.58751.3248-0.23390.62281.44390.8386-0.2516-0.3592-0.7688-0.07110.48550.1991-0.052-0.05050.01510.12090.795719.7186-7.16826.4997
39.6961-7.77450.29749.251-1.49180.52970.30012.55480.197-0.51060.43190.695-0.25240.6608-0.7320.2925-0.06470.05341.06330.33130.720222.8281-11.8142-16.8498
43.3347-4.4585.22135.9599-6.98028.1753-0.85630.8725-0.46070.0498-0.59570.62680.00191.77411.45190.0828-0.11430.56480.36420.66020.813716.1581-6.776-15.5416
517.7314-2.51229.404615.2621-6.12836.5311-0.0878-0.62590.89221.7452-0.89740.72-0.2893-0.67960.98520.2948-0.03130.23050.03020.05050.35844.5812-13.76740.7975
62.754-6.973615.304117.7118-38.279389.25970.1917-0.07961.6088-0.2784-1.2302-0.9408-0.0525-0.3021.0385-0.05550.09970.113-0.10060.19041.05716.9239-6.0664-6.6091
767.4172-8.4123-3.38992.3776-12.6565128.9986-0.1652.00030.62171.16690.81461.0728-0.447-2.3739-0.64960.6472-0.0284-0.05790.38320.29480.915117.0510.0827-17.0373
818.311329.3358-11.183149.1414-12.888418.6216-0.310.33641.4595-1.9215-0.21050.2708-1.0118-0.54980.52050.18230.06720.06670.32870.29971.03039.60371.3263-9.5386
93.36960.67736.3250.18120.785517.1151-0.805-0.21451.44761.33031.9721-0.1162-0.43361.3856-1.16710.10090.00930.12270.05770.19111.04486.5426-0.2561-0.232
1069.0957-36.3259-33.191619.097717.449915.9443-3.386-3.1661-3.1285-2.2781.78274.09491.85353.63651.60330.4633-0.21140.2680.65730.45171.571223.3872-2.2165-10.2021
110.8127-0.39893.30695.99220.30614.0982-0.37280.17741.49070.3761-0.47550.1553-0.342-0.02740.8482-0.1622-0.0120.0683-0.05650.16931.198615.3253-4.35561.9913
125.5079-0.64431.44549.5101-10.571511.9047-0.51661.40131.4538-0.9531-0.21590.15480.8186-0.15450.73250.0202-0.09590.10930.26630.33640.733211.0303-11.161-10.4493
13175.0918-35.620465.297336.1343-45.837100.819-3.42221.92511.6729-0.5430.49240.8558-3.83070.13762.92990.1484-0.34460.10960.49570.90460.84283.1654-11.4993-23.5395
141.1922.66340.11675.95080.26080.0114-0.081.9490.7734-0.4962-0.35080.16841.20011.40830.43080.3860.12020.4450.61090.65210.492111.9493-15.7938-13.2801
152.3848-1.24351.4388.2969-1.08873.77460.0613-0.22480.17110.639-0.30520.3850.30620.1710.2439-0.0131-0.05280.17570.01540.02270.293220.0463-30.200714.0894
162.3089-3.748-0.73612.16783.67431.2452-0.08440.33550.450.0177-0.1695-0.83180.194-0.39980.25390.2079-0.0830.08440.2371-0.0180.270520.1831-31.772211.2916
176.2585-2.523-1.94257.971.27594.02490.02530.42540.0974-0.5015-0.1871-0.3679-0.20180.03860.16190.1975-0.04980.08720.08450.05410.070418.9685-34.57416.2316
181.52440.13081.39175.7983-2.40352.37040.17290.25780.0363-0.223-0.3294-0.78480.24840.33650.15650.1234-0.03930.06950.0841-0.01510.202221.4651-39.600110.1648
198.3353-4.1121-6.19669.80378.03137.78910.2458-0.09480.5605-0.1352-0.0946-1.0997-0.17550.5052-0.15120.3416-0.27920.07820.07070.10180.354128.0124-25.94049.2345
2011.15329.26481.628928.63423.02321.81240.1008-0.0008-1.39560.3719-1.2625-3.20520.34810.82871.16170.08040.02930.02410.23920.04970.198727.7795-42.492114.9777
213.1218-3.5895-0.197513.39312.92182.30750.12910.52410.4657-0.4473-0.48271.2286-0.1616-0.07150.35350.12570.03720.00470.2690.09380.2449-7.0978-24.6327-9.035
2212.2057-3.29561.74714.2668-1.25092.78590.20291.24691.5091-0.6009-0.4934-0.23450.23310.02580.29050.2580.07820.11920.20770.26720.22622.2806-19.0039-12.7728
231.06044.67161.824120.58098.03623.1379-0.41020.91161.0282-0.259-0.23670.3190.27180.7250.64690.4880.14170.14320.73770.41550.04073.3536-22.3532-21.8411
244.2859-3.0223-1.396725.18780.06650.49180.02210.94840.697-1.36760.15840.27890.142-0.0536-0.18050.32910.0814-0.01370.5030.1717-0.0942-4.2813-26.7377-17.7573
255.51440.61733.34274.4166-0.89112.3945-0.22370.87721.42450.0238-0.1323-0.3983-0.0503-0.02690.35590.09130.0750.16130.14810.33160.24851.2202-17.6665-10.9486
268.25221.6142-2.071250.8623-6.29211.20550.36990.660.47510.4340.0183-0.36320.2391-0.181-0.38820.11760.05150.05070.19670.0677-0.0959-2.2063-29.578-4.4408
273.59020.24563.23282.654-0.26155.26870.2388-0.19170.1430.1909-0.2888-0.39270.18630.18130.050.1098-0.05780.10340.075-0.04280.023513.6328-41.186415.4783
286.1823-3.19197.35663.21550.278719.3574-0.2298-0.3385-0.11090.1322-0.07150.5426-1.1394-0.91640.30130.1601-0.08310.05840.0628-0.0267-0.04130.9086-39.331712.3441
291.0089-0.82110.19993.3312-0.89397.2248-0.0113-0.04290.06810.13660.133-0.1121-0.8262-0.2176-0.12170.0967-0.01320.03680.0472-0.021-0.00717.8595-36.903915.774
305.94190.35597.82852.11962.237515.3065-0.208-0.2327-0.09840.2644-0.0067-0.24810.2412-0.03220.21460.1604-0.05880.12490.09880.08770.00458.776-45.981523.0695
3119.8909-20.909115.582381.083632.969853.4122-0.98392.22662.17385.3536-1.38031.549-1.0652-4.63872.36420.5121-0.51230.2880.63760.45210.78615.33010.1494-16.3402
3286.758917.99133.642952.8467-25.563328.14322.68910.93194.15361.576-3.0331-1.57991.945-1.97190.34390.6844-0.17860.17590.45810.08670.77178.07763.0767-22.1957
3386.363316.710549.290249.806179.176169.50171.54045.43692.6782-3.50950.48167.1551.01930.0422-2.0220.9844-0.1743-0.27020.63370.3110.8754-0.58677.0701-22.6796
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1HA1 - 81 - 8
2X-RAY DIFFRACTION2HA9 - 219 - 21
3X-RAY DIFFRACTION3HA22 - 2822 - 28
4X-RAY DIFFRACTION4HA29 - 3629 - 36
5X-RAY DIFFRACTION5HA37 - 4537 - 45
6X-RAY DIFFRACTION6HA46 - 5046 - 50
7X-RAY DIFFRACTION7HA51 - 5651 - 56
8X-RAY DIFFRACTION8HA57 - 6157 - 61
9X-RAY DIFFRACTION9HA62 - 6862 - 68
10X-RAY DIFFRACTION10HA69 - 7769 - 77
11X-RAY DIFFRACTION11HA78 - 8978 - 89
12X-RAY DIFFRACTION12HA90 - 10290 - 102
13X-RAY DIFFRACTION13HA103 - 107103 - 107
14X-RAY DIFFRACTION14HA108 - 115108 - 115
15X-RAY DIFFRACTION15HA116 - 141116 - 141
16X-RAY DIFFRACTION16HA142 - 162142 - 162
17X-RAY DIFFRACTION17HA163 - 180163 - 180
18X-RAY DIFFRACTION18HA181 - 203181 - 203
19X-RAY DIFFRACTION19HA204 - 214204 - 214
20X-RAY DIFFRACTION20HA215 - 226215 - 226
21X-RAY DIFFRACTION21LB1 - 241 - 24
22X-RAY DIFFRACTION22LB25 - 4625 - 46
23X-RAY DIFFRACTION23LB47 - 5747 - 57
24X-RAY DIFFRACTION24LB58 - 7758 - 77
25X-RAY DIFFRACTION25LB78 - 9778 - 97
26X-RAY DIFFRACTION26LB98 - 10698 - 106
27X-RAY DIFFRACTION27LB107 - 138107 - 138
28X-RAY DIFFRACTION28LB139 - 147139 - 147
29X-RAY DIFFRACTION29LB148 - 183148 - 183
30X-RAY DIFFRACTION30LB184 - 213184 - 213
31X-RAY DIFFRACTION31PC167 - 1725 - 10
32X-RAY DIFFRACTION32PC173 - 17811 - 16
33X-RAY DIFFRACTION33PC179 - 18317 - 21

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