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- PDB-4zfo: J22.9-xi: chimeric mouse/human antibody against human BCMA (CD269) -

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Basic information

Entry
Database: PDB / ID: 4zfo
TitleJ22.9-xi: chimeric mouse/human antibody against human BCMA (CD269)
Components
  • (J22.9-xi Fab, Light ...) x 2
  • J22.9-xi Fab, Heavy Chain
  • Tumor necrosis factor receptor superfamily member 17
KeywordsIMMUNE SYSTEM / antibody Fab-ligand complex anti-BCMA anti-tumor
Function / homology
Function and homology information


lymphocyte homeostasis / TNFs bind their physiological receptors / endomembrane system / tumor necrosis factor-mediated signaling pathway / signaling receptor activity / adaptive immune response / signal transduction / membrane / plasma membrane
Similarity search - Function
BCMA, TALL-1 binding / Tumour necrosis factor receptor 17 / BCMA, TALL-1 binding / Tumor necrosis factor receptor 13C/17 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Tumor necrosis factor receptor superfamily member 17
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.895 Å
AuthorsMarino, S.F. / Daumke, O. / Olal, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
HFSPO Germany
CitationJournal: Mol Oncol / Year: 2015
Title: Potent anti-tumor response by targeting B cell maturation antigen (BCMA) in a mouse model of multiple myeloma.
Authors: Oden, F. / Marino, S.F. / Brand, J. / Scheu, S. / Kriegel, C. / Olal, D. / Takvorian, A. / Westermann, J. / Yilmaz, B. / Hinz, M. / Daumke, O. / Hopken, U.E. / Muller, G. / Lipp, M.
History
DepositionApr 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Tumor necrosis factor receptor superfamily member 17
L: J22.9-xi Fab, Light Chain
H: J22.9-xi Fab, Heavy Chain
B: J22.9-xi Fab, Light Chain
A: J22.9-xi Fab, Heavy Chain
K: Tumor necrosis factor receptor superfamily member 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,71311
Polymers106,1046
Non-polymers6095
Water13,854769
1
F: Tumor necrosis factor receptor superfamily member 17
B: J22.9-xi Fab, Light Chain
A: J22.9-xi Fab, Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2895
Polymers53,0163
Non-polymers2732
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-44 kcal/mol
Surface area20980 Å2
MethodPISA
2
L: J22.9-xi Fab, Light Chain
H: J22.9-xi Fab, Heavy Chain
K: Tumor necrosis factor receptor superfamily member 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4246
Polymers53,0873
Non-polymers3363
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-45 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.801, 110.139, 137.279
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules FK

#1: Protein Tumor necrosis factor receptor superfamily member 17 / B-cell maturation protein / BCMA / CD269


Mass: 5903.708 Da / Num. of mol.: 2
Fragment: Extracellular (N-terminal) domain, UNP residues 1-54
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF17, BCM, BCMA / Plasmid: pGEX6p-1
Details (production host): N-terminal glutathione-S-transferase (GST) fusion
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: Q02223

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Antibody , 3 types, 4 molecules LHAB

#2: Antibody J22.9-xi Fab, Light Chain


Mass: 23542.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fab Light Chain fragment of anti-BCMA antibody J22.9-xi
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pTT5 / Details (production host): 6x EBNA protein binding sites / Cell line (production host): HEK293_6E / Production host: Homo sapiens (human)
#3: Antibody J22.9-xi Fab, Heavy Chain


Mass: 23641.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fab Heavy Chain fragment of anti-BCMA antibody J22.9-xi
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pTT5 / Details (production host): 6x EBNA protein binding sites / Cell line (production host): HEK293_6E / Production host: Homo sapiens (human)
#4: Antibody J22.9-xi Fab, Light Chain


Mass: 23471.057 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fab Light Chain fragment of anti-BCMA antibody J22.9-xi
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pTT5 / Details (production host): 6x EBNA protein binding sites / Cell line (production host): HEK293_6E / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 774 molecules

#5: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#6: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 769 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 52.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1 microliter of the complex at 8 mg/ml with 2 microliters of 21% PEG 3350, 0.1 M BisTris pH 6.5 and 5 mM CuCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.895→42.268 Å / Num. obs: 87925 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 10.46
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.76 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHASERCCP4Interface 2.1.0phasing
XDSJuly 4, 2012data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EO9
Resolution: 1.895→42.258 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 19.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.209 4396 5 %
Rwork0.1762 --
obs0.1779 87918 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.895→42.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7072 0 31 769 7872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017365
X-RAY DIFFRACTIONf_angle_d1.2029999
X-RAY DIFFRACTIONf_dihedral_angle_d14.1272653
X-RAY DIFFRACTIONf_chiral_restr0.0481120
X-RAY DIFFRACTIONf_plane_restr0.0061287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8955-1.9170.35131320.29512508X-RAY DIFFRACTION90
1.917-1.93960.28821460.2552765X-RAY DIFFRACTION100
1.9396-1.96320.27551460.23842785X-RAY DIFFRACTION100
1.9632-1.98810.27811430.22132705X-RAY DIFFRACTION100
1.9881-2.01420.22961450.21442764X-RAY DIFFRACTION100
2.0142-2.04180.24261470.21712789X-RAY DIFFRACTION100
2.0418-2.0710.26661450.20372752X-RAY DIFFRACTION100
2.071-2.10190.23651450.18992752X-RAY DIFFRACTION100
2.1019-2.13480.20991450.18932752X-RAY DIFFRACTION100
2.1348-2.16980.26831450.1882763X-RAY DIFFRACTION100
2.1698-2.20720.26581470.1862797X-RAY DIFFRACTION100
2.2072-2.24730.22541450.18872745X-RAY DIFFRACTION100
2.2473-2.29050.22871460.18772783X-RAY DIFFRACTION100
2.2905-2.33730.20181460.17692762X-RAY DIFFRACTION100
2.3373-2.38810.20851450.17892765X-RAY DIFFRACTION100
2.3881-2.44360.20871480.17492809X-RAY DIFFRACTION100
2.4436-2.50470.23191470.18152789X-RAY DIFFRACTION100
2.5047-2.57240.22591450.17982751X-RAY DIFFRACTION100
2.5724-2.64810.20521460.18492786X-RAY DIFFRACTION100
2.6481-2.73360.23041460.18242774X-RAY DIFFRACTION100
2.7336-2.83130.22831480.18512801X-RAY DIFFRACTION100
2.8313-2.94460.19891470.17382804X-RAY DIFFRACTION100
2.9446-3.07860.20061470.18182791X-RAY DIFFRACTION100
3.0786-3.24080.22081480.17442803X-RAY DIFFRACTION100
3.2408-3.44380.21271480.17172819X-RAY DIFFRACTION100
3.4438-3.70960.19211490.16252820X-RAY DIFFRACTION100
3.7096-4.08260.17531490.1522844X-RAY DIFFRACTION100
4.0826-4.67270.14771500.12912840X-RAY DIFFRACTION100
4.6727-5.88460.17181510.13592883X-RAY DIFFRACTION100
5.8846-42.26810.15581590.16563021X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
17.90610.7299-2.0537.3758-5.44924.3184-0.47730.51551.0882-0.6570.33250.1841-1.0118-0.64560.12990.51180.0593-0.13910.3570.18430.4601-56.22433.7372-55.0693
25.5783-2.14475.04973.9365-1.68988.7554-0.09170.20920.5536-0.1020.00690.1725-0.35840.2760.16290.1162-0.0252-0.04280.11380.0310.203-52.7153-1.3948-46.9005
35.75653.25382.92555.73781.74498.1854-0.03120.54780.131-0.56310.07450.47290.8937-0.07260.00770.3381-0.0209-0.05630.2010.01240.186-52.715-5.4574-54.4699
45.2272-1.8725-2.62751.21110.29772.0873-0.40660.9402-0.504-0.9124-0.20630.79220.1711-0.5060.55860.582-0.2012-0.13410.4625-0.09210.3919-58.9223-12.6131-54.8218
53.3927-1.8328-1.09562.4129-0.07584.4402-0.06171.60490.2216-1.16090.14911.3078-0.0001-1.1762-0.13470.5785-0.1353-0.32430.6360.17570.6719-60.3512-5.4566-59.1391
62.9469-3.5375-0.77615.7451.34611.3351-0.01160.02310.25340.1440.1155-0.7609-0.04180.149-0.09570.1219-0.0059-0.04250.15840.00280.25752.485915.4441-27.9193
70.26730.61440.50122.20580.52341.42920.01260.08580.03960.0799-0.0138-0.1042-0.0507-0.03320.00930.07030.03790.02040.14170.02360.1482-5.986415.4461-33.2842
81.2508-1.1448-1.79822.4892.52813.69080.11550.05260.02440.0446-0.0323-0.2247-0.15120.0285-0.07220.08750.025-0.04530.12860.00870.1554-3.251414.3784-23.3513
90.78630.6847-0.72354.6383-3.9465.3591-0.0613-0.05340.0825-0.15970.01980.06210.047-0.04940.08580.1732-0.0061-0.01690.1329-0.03530.0837-12.953113.35023.436
100.3828-0.28760.13283.5592-1.85013.79860.1037-0.06070.006-0.2097-0.0177-0.0734-0.02890.292-0.06930.1005-0.02340.00620.178-0.02750.1054-10.141615.1178-4.1131
111.38121.3019-0.71554.6455-2.69263.94950.0615-0.1680.03860.2349-0.1527-0.0347-0.29010.33050.06570.164-0.0281-0.02060.2039-0.00970.106-9.354913.56919.2893
120.46140.7155-0.39133.3625-3.53389.13130.0068-0.05750.0033-0.07980.3070.33820.0614-0.6872-0.34740.1012-0.0355-0.00510.1587-0.01890.159-19.2782-6.0886-26.4897
131.33070.3222-0.02712.61850.33082.17790.09740.1139-0.10070.01590.037-0.14620.31770.0459-0.13910.10760.0226-0.0070.1338-0.00640.0844-10.8837-3.8028-35.0506
146.68271.33131.21332.35710.48413.45490.1339-0.165-0.46780.2034-0.0028-0.33980.59550.2423-0.1320.23520.0733-0.02090.1303-0.01620.1466-7.5085-10.8779-33.3009
151.3050.2328-0.73723.132-1.23563.8657-0.02860.0649-0.06790.06-0.0091-0.03080.18570.04290.01480.07430.0066-0.01460.1179-0.02810.0881-12.89-2.0357-31.4705
160.9583-0.4828-0.34362.93010.20972.1612-0.033-0.05090.1264-0.0531-0.01280.1673-0.1824-0.17780.0480.13160.0223-0.05220.1564-0.01820.1128-24.07829.0741-2.6603
174.76222.78042.90481.77091.75551.86420.0446-0.41830.6180.3952-0.56210.84150.0913-0.72650.49990.26110.02610.02440.2253-0.03780.2111-31.73287.81642.371
180.33280.3432-0.45762.7687-0.12711.3990.00320.0476-0.0455-0.106-0.01250.03450.0575-0.0116-0.00180.0798-0.0033-0.04430.1019-0.01070.1382-51.3488-18.2294-39.5295
190.6452-1.08960.46054.2516-1.54940.98620.07780.08040.0313-0.2883-0.0828-0.04580.15010.06330.01220.0904-0.0076-0.02310.1235-0.02940.1515-48.1864-22.2062-34.7572
201.6309-0.18680.60161.59520.38783.45090.0849-0.3281-0.16680.5134-0.10030.1220.0862-0.36050.00390.2842-0.06080.02420.18260.01610.1902-42.1764-35.8016-8.6019
211.38730.11311.11531.99680.29092.6329-0.01650.05420.126-0.14690.0211-0.0667-0.15610.18360.0110.0915-0.0220.00260.1163-0.01710.1353-40.8658-0.6672-30.1204
226.27312.8718-1.08816.0553-1.05924.188-0.2597-0.39510.1999-0.056-0.0850.423-0.0486-0.13860.28420.1230.0283-0.01640.0822-0.04060.1507-46.94614.7836-27.1635
230.5849-0.05940.75951.6231-0.35854.94820.03360.05610.09610.02350.0679-0.0007-0.070.0265-0.08730.0421-0.02170.01630.1144-0.00660.1328-41.0535-3.3663-30.3715
240.9718-1.13110.06595.99271.42791.1057-0.03950.028-0.14870.38060.044-0.05590.13610.0575-0.02690.1486-0.0204-0.010.1536-0.00870.1412-30.8797-27.2335-12.3666
250.8368-0.25320.16526.18911.0861.53740.04380.0241-0.21490.45470.0967-1.1290.14890.2116-0.12210.17270.0071-0.0710.1927-0.0390.3023-21.6415-28.4105-10.9414
262.04831.67772.29343.71123.74194.0537-0.42620.2617-0.8915-1.2836-0.4353-0.23340.30660.14550.80280.42930.17580.18180.7092-0.00980.44262.52384.1083-56.0743
276.11482.3189-1.47755.0815-0.09219.6503-0.0430.76770.2841-0.66330.0738-0.38440.06770.55310.06060.21190.03860.05440.34440.03170.2025-0.67597.4965-48.6769
282.7928-2.66532.94952.548-2.81493.115-0.41030.36270.1776-0.5263-0.1545-0.5655-0.42850.46660.54020.7309-0.09510.08270.66960.27880.68835.807417.7762-47.52
292.1614-2.02920.69963.08050.1973.8436-0.24662.29340.9765-1.70490.463-1.2034-0.22351.3123-0.19770.6662-0.06960.2381.15890.08020.77557.370213.6122-54.8035
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'F' and (resid 6 through 11 )
2X-RAY DIFFRACTION2chain 'F' and (resid 12 through 19 )
3X-RAY DIFFRACTION3chain 'F' and (resid 20 through 27 )
4X-RAY DIFFRACTION4chain 'F' and (resid 28 through 34 )
5X-RAY DIFFRACTION5chain 'F' and (resid 35 through 41 )
6X-RAY DIFFRACTION6chain 'L' and (resid 1 through 32 )
7X-RAY DIFFRACTION7chain 'L' and (resid 33 through 90 )
8X-RAY DIFFRACTION8chain 'L' and (resid 91 through 113 )
9X-RAY DIFFRACTION9chain 'L' and (resid 114 through 150 )
10X-RAY DIFFRACTION10chain 'L' and (resid 151 through 174 )
11X-RAY DIFFRACTION11chain 'L' and (resid 175 through 214 )
12X-RAY DIFFRACTION12chain 'H' and (resid 1 through 17 )
13X-RAY DIFFRACTION13chain 'H' and (resid 18 through 57 )
14X-RAY DIFFRACTION14chain 'H' and (resid 58 through 76 )
15X-RAY DIFFRACTION15chain 'H' and (resid 77 through 118 )
16X-RAY DIFFRACTION16chain 'H' and (resid 119 through 210 )
17X-RAY DIFFRACTION17chain 'H' and (resid 211 through 221 )
18X-RAY DIFFRACTION18chain 'B' and (resid 1 through 75 )
19X-RAY DIFFRACTION19chain 'B' and (resid 76 through 113 )
20X-RAY DIFFRACTION20chain 'B' and (resid 114 through 213 )
21X-RAY DIFFRACTION21chain 'A' and (resid 1 through 57 )
22X-RAY DIFFRACTION22chain 'A' and (resid 58 through 76 )
23X-RAY DIFFRACTION23chain 'A' and (resid 77 through 118 )
24X-RAY DIFFRACTION24chain 'A' and (resid 119 through 195 )
25X-RAY DIFFRACTION25chain 'A' and (resid 196 through 220 )
26X-RAY DIFFRACTION26chain 'K' and (resid 7 through 11 )
27X-RAY DIFFRACTION27chain 'K' and (resid 12 through 27 )
28X-RAY DIFFRACTION28chain 'K' and (resid 28 through 34 )
29X-RAY DIFFRACTION29chain 'K' and (resid 35 through 41 )

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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