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- PDB-9gfh: BCR Fab from the subset 1 chronic lymphocytic leukaemia case P1173 -

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Basic information

Entry
Database: PDB / ID: 9gfh
TitleBCR Fab from the subset 1 chronic lymphocytic leukaemia case P1173
Components
  • BCR P1173 heavy chain
  • BCR P1173 light chain
KeywordsIMMUNE SYSTEM / B-cell receptor / Fab fragment / chronic lymphocytic leukaemia
Function / homologyCITRIC ACID
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsCocomazzi, P.G. / Degano, M.
Funding support Italy, United Kingdom, 4items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchIG17032 Italy
Italian Association for Cancer ResearchIG25764 Italy
Italian Ministry of HealthRF-2018-12368231 Italy
Worldwide Cancer Research19-0096 United Kingdom
CitationJournal: To Be Published
Title: Defective cell-autonomous signalling and antigenic polyreactivity of B-cell receptors from chronic lymphocytic leukaemia stereotyped subset 1
Authors: Cocomazzi, P.G. / Iatrou, A. / Minici, C. / Degano, M.
History
DepositionAug 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: BCR P1173 light chain
A: BCR P1173 heavy chain
B: BCR P1173 light chain
D: BCR P1173 light chain
F: BCR P1173 light chain
H: BCR P1173 heavy chain
C: BCR P1173 heavy chain
E: BCR P1173 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,63213
Polymers192,2068
Non-polymers1,4265
Water25214
1
L: BCR P1173 light chain
H: BCR P1173 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8144
Polymers48,0512
Non-polymers7632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: BCR P1173 heavy chain
B: BCR P1173 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2733
Polymers48,0512
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: BCR P1173 light chain
C: BCR P1173 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2733
Polymers48,0512
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: BCR P1173 light chain
E: BCR P1173 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2733
Polymers48,0512
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.416, 128.509, 134.650
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-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "C" and (resid 1 through 167 or resid 175...
d_3ens_1(chain "E" and (resid 1 through 167 or resid 175 through 224 or resid 225))
d_4ens_1(chain "H" and (resid 1 through 167 or resid 175...
d_1ens_2chain "B"
d_2ens_2(chain "D" and (resid 2 through 93 or resid 96 through 214))
d_3ens_2(chain "F" and (resid 2 through 93 or resid 96 through 214))
d_4ens_2(chain "L" and (resid 2 through 93 or resid 96 through 214))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLUGLUPROPROAB1 - 2241 - 224
d_12ens_1NAGNAGNAGNAGAJ301
d_21ens_1GLUGLUASNASNCG1 - 1671 - 167
d_22ens_1GLYGLYVALVALCG175 - 198175 - 198
d_23ens_1ASPASPPROPROCG203 - 224203 - 224
d_24ens_1NAGNAGNAGNAGCL301
d_31ens_1GLUGLUASNASNEH1 - 1671 - 167
d_32ens_1GLYGLYPROPROEH175 - 224175 - 224
d_33ens_1NAGNAGNAGNAGEM301
d_41ens_1GLUGLUASNASNHF1 - 1671 - 167
d_42ens_1GLYGLYVALVALHF175 - 198175 - 198
d_43ens_1ASPASPPROPROHF203 - 224203 - 224
d_44ens_1NAGNAGNAGNAGGI1
d_11ens_2ILEILEGLUGLUBC2 - 2142 - 214
d_21ens_2ILEILESERSERDD2 - 932 - 93
d_22ens_2PROPROGLUGLUDD96 - 21496 - 214
d_31ens_2ILEILESERSERFE2 - 932 - 93
d_32ens_2PROPROGLUGLUFE96 - 21496 - 214
d_41ens_2ILEILESERSERLA2 - 932 - 93
d_42ens_2PROPROGLUGLULA96 - 21496 - 214

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.941683249698, 0.320730354047, 0.101807157073), (-0.198419794425, -0.284893655602, -0.937798054049), (-0.271776088755, -0.903309274275, 0.331918834342)11.7280621306, -80.8089466982, -29.0441325781
2given(0.966917447414, -0.247793544518, -0.0605723466824), (-0.210391325468, -0.908951374804, 0.359920669605), (-0.144243336259, -0.335269678821, -0.931014555422)87.6454547312, -123.171586246, 16.5415580119
3given(0.995883174243, -0.000305946558977, -0.0906455164694), (0.09059239146, 0.037756535162, 0.99517207691), (0.00311799115733, -0.999286920984, 0.037628814516)30.2381449392, -26.6276143502, -32.57340628
4given(-0.965422075385, 0.259367160508, 0.0262467599739), (-0.106927028637, -0.302149320584, -0.947244635043), (-0.237753710604, -0.917297369516, 0.319434983954)6.83353374141, -79.1400950328, -28.4410055541
5given(0.982166752577, -0.187851948637, 0.007753420306), (-0.178057851261, -0.916135473688, 0.359153442772), (-0.0603644906996, -0.354129127924, -0.933246317442)92.0349584845, -122.089104269, 17.8511976413
6given(0.998399052597, 0.0251466272109, -0.0506653620743), (0.0497549536593, 0.0355976469749, 0.998126871753), (0.0269030920261, -0.999049775872, 0.0342894877428)31.97978731, -28.2024296094, -31.7720142645

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Components

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Antibody / Protein , 2 types, 8 molecules LBDFAHCE

#1: Antibody
BCR P1173 light chain


Mass: 23421.916 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Protein
BCR P1173 heavy chain


Mass: 24629.566 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Sugars , 2 types, 4 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 15 molecules

#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.82 Å3/Da / Density % sol: 56.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M citric acid pH 5 20% PEG 6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.87→91.77 Å / Num. obs: 123151 / % possible obs: 96.2 % / Redundancy: 13.4 % / Biso Wilson estimate: 61.46 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.034 / Net I/σ(I): 12.4
Reflection shellResolution: 1.87→2.02 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6158 / CC1/2: 0.666 / Rpim(I) all: 0.399 / % possible all: 81.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→91.77 Å / SU ML: 0.3048 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.8872
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 1997 4.77 %RANDOM
Rwork0.2137 39882 --
obs0.2151 41879 70.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.46 Å2
Refinement stepCycle: LAST / Resolution: 2.72→91.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13101 0 93 14 13208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002813507
X-RAY DIFFRACTIONf_angle_d0.644818339
X-RAY DIFFRACTIONf_chiral_restr0.04772039
X-RAY DIFFRACTIONf_plane_restr0.00512331
X-RAY DIFFRACTIONf_dihedral_angle_d13.54634876
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BAX-RAY DIFFRACTIONTorsion NCS0.660977485683
ens_1d_3BAX-RAY DIFFRACTIONTorsion NCS0.746964549156
ens_1d_4BAX-RAY DIFFRACTIONTorsion NCS0.459973997729
ens_2d_2CBX-RAY DIFFRACTIONTorsion NCS0.617521389344
ens_2d_3CBX-RAY DIFFRACTIONTorsion NCS0.583907791047
ens_2d_4CBX-RAY DIFFRACTIONTorsion NCS0.421008159727
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-2.780.3013120.3596383X-RAY DIFFRACTION9.43
2.78-2.860.3218370.3358758X-RAY DIFFRACTION18.98
2.86-2.940.3494760.32591295X-RAY DIFFRACTION32.91
2.94-3.040.36531110.31742085X-RAY DIFFRACTION52.4
3.04-3.150.31241320.30522580X-RAY DIFFRACTION64.91
3.15-3.270.33551500.28333085X-RAY DIFFRACTION77.04
3.27-3.420.32090.2753820X-RAY DIFFRACTION96.36
3.42-3.60.31511620.25172479X-RAY DIFFRACTION62.36
3.6-3.830.27251750.23382781X-RAY DIFFRACTION70.08
3.83-4.120.23251950.20254021X-RAY DIFFRACTION100
4.12-4.540.1961870.1574073X-RAY DIFFRACTION99.95
4.54-5.20.18531810.14554096X-RAY DIFFRACTION100
5.2-6.550.18711750.19174121X-RAY DIFFRACTION100
6.55-91.770.23631950.23964305X-RAY DIFFRACTION99.82
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)
14.567068163031.30866738631-0.1084334707433.60645394954-0.6810045915376.432243710720.0157554548132-0.293105665382-0.1039162091090.225519041832-0.003044674453640.394680001668-0.0120286878385-0.334444521590.009275896655110.19565206015-0.004610800472020.00257650249580.249072462698-0.0264315163880.323133050236-21.0044357668-41.531069615519.0497000309
24.51825023746-1.135197197110.2905580933914.414805137630.02603148942344.555093701570.1959586340690.212530435058-0.448254927004-0.140143123435-0.05571647491680.2018493378410.356435353872-0.207557105339-0.06324087352930.227384815206-0.0511944887995-0.03745455385960.198200416459-0.01129556081040.2242051148230.756225183702-43.74355877814.4596641781
31.608230660390.6344241098760.4668091100069.838712209240.164233027072.19930710980.0430327453986-0.0378365015998-0.1504577243660.09987633737360.02461923606680.2305632300090.102671443262-0.0296870211787-0.07793118085250.201018673390.0653531150136-0.05162866550270.4138763818560.05545382060860.319777794725-52.2747260764-52.0516069749-8.27528975316
46.56801925625-2.10667834231-0.2708089104244.34713902709-0.5080040301593.367098873850.2152110893980.2461103436640.114108732105-0.247413704708-0.177079494483-0.374604778473-0.0833071056904-0.132274057396-0.05779034645570.2007492927360.0606096072856-0.09045890035560.287851050261-0.009390392536790.388578529778-30.2860389045-47.6161599599-11.9625823716
53.491063886581.865539096741.883862011543.775041591651.672735248954.736688006540.1186436764760.393452618746-0.0647261939748-0.2258253214080.00754988167132-0.504698434530.06877156273470.361690413502-0.1067502192580.2999506502020.07073215258350.00656985012750.4250969709320.07122589794440.57109935576343.4561735272-47.788349188629.3474761493
66.80636666031-0.738585096423-0.5941224839544.20826994509-0.03566008534695.4330750562-0.1090335680660.4062794425860.00576776045289-0.825783043965-0.114423423173-0.2292830096590.05725128278920.5512079816320.1929593204730.511910140399-0.0434955568605-0.02829508735650.2903518680690.01692386811870.24716844827623.8861615779-49.795798121618.3846252891
75.86734147862-1.53298629309-0.2546065985565.351994755741.057756668694.059066405310.06490715450260.579520524704-0.360251707538-0.18191540311-0.1456272809920.07845457325570.286257399985-0.387290885530.09951724033650.253686999191-0.042649827468-0.06556781340130.5889775659690.03339375483030.43981488585550.4553611966-67.953895281349.2857010922
86.570493968180.46803469168-1.219929473576.07675052971-0.595583865245.25777874517-0.08475693377620.121279099312-0.5577361774-0.1514648740960.05580660056760.6890126173260.678337898014-0.1738751029960.04979154279150.3543032018350.07801052059580.008599133595690.324697608517-0.05771871700980.45797583669170.6106770344-77.696844495348.009157534
92.592925773160.639264484695-0.2597964644095.820507881711.5711964351.83361344108-0.162609170808-0.03025576234970.3209154769620.2509154757840.143235938554-0.0607688987018-0.127704393635-0.1697610577990.02895732919510.6763706635290.18060463827-0.02334940541440.458161136712-0.006418993610080.353397256114-8.59558161766-19.790723703541.4607080311
104.959313816560.344446594543-2.482681789690.7212467370340.4640476626546.51493103518-0.0361936721478-0.827885987202-0.165422651370.7050589633440.0700002152102-0.148941124065-0.1465355868270.2303487026380.003434656969730.844939407040.108293812446-0.1713901962480.3963570815640.005728732070930.451048730793.28537023206-29.322805087249.487476389
113.715452299790.1185565106240.01407253877913.62345706595-1.153918699652.033953237310.107897662313-1.54085947063-0.2598743493780.7278424902040.0348820082140.0781772695190.0942104198726-0.0318872090293-0.2202561946120.6160167822810.0814391320730.07332387549330.8928457174170.2091993827420.514489925433-38.7375188603-74.406784581712.1160448829
124.349778895630.760453491183-0.1773737485277.32850792735-1.108201180444.30674649973-0.138331881114-0.336010448342-0.5779950428620.06125493364120.0784686048068-0.06548885287960.2888729718490.293381183650.03068412254070.2961061495360.0565661295699-0.001577232441570.430784775210.1003794165120.31490590075625.1444380795-64.229067335952.3140120249
133.50336431529-0.4005684342690.4149723446452.63108740404-1.019464152971.32378853082-0.0144982745458-0.542453953138-1.067198855380.187660754165-0.124101388508-0.1580223173280.4004554180760.1430014944520.1462534850510.6090149292570.1258651898580.02996250689530.6615816292810.3268730274640.758393306207-26.503534113-81.93230367863.08766999033
144.310694016730.410481506031.840924593641.826613879920.5630315195756.79227673931-0.169318542023-0.4999950444070.3298667877290.32774380635-0.01618580661830.138374617617-0.2244178918010.06057261994260.176560268940.369639688280.0303964974081-0.004666081379440.2620437926780.05887644436140.45843852893711.198609346-54.512189385454.1194464032
154.038756137940.03214670083820.3328928115533.843032032670.1334775244064.52862348969-0.363606369620.7660757372190.202241353459-0.3122832712720.09347684944220.0710382860366-0.2265057851670.1459848985090.2994578791330.393983319494-0.0260598110633-0.05183032345140.5852537301720.194040686250.63219412927268.2946436913-43.432847547335.1946969316
163.24069919118-0.525546804935-1.01795523976.011774693740.9680339562112.70470268199-0.103457300983-0.04702032892440.50874006888-0.08694432947780.0643453050551-0.183453688949-0.172033742840.3096572535560.0164494460680.3445337673650.002308489518380.01240988220930.5351166923130.1138418162660.5733992362281.5100357039-40.994930589345.5991204604
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'H' and resid 1 through 120)HG1 - 1201 - 120
22(chain 'L' and resid 1 through 108)LA1 - 1081 - 108
33(chain 'A' and resid 1 through 120)AB1 - 1201 - 120
44(chain 'B' and resid 2 through 108)BD2 - 1081 - 105
55(chain 'C' and resid 1 through 120)CL1 - 1201 - 120
66(chain 'D' and resid 1 through 108)DE1 - 1081 - 108
77(chain 'E' and resid 1 through 120)EN1 - 1201 - 120
88(chain 'F' and resid 1 through 108)FF1 - 1081 - 108
99(chain 'H' and resid 121 through 224)HG121 - 224121 - 217
1010(chain 'L' and resid 109 through 214)LA109 - 214109 - 214
1111(chain 'A' and resid 121 through 224)AB121 - 224121 - 206
1212(chain 'C' and resid 121 through 224)CL121 - 224121 - 215
1313(chain 'B' and resid 109 through 214)BD109 - 214106 - 211
1414(chain 'D' and resid 109 through 214)DE109 - 214109 - 214
1515(chain 'E' and resid 121 through 224)EN121 - 224121 - 213
1616(chain 'F' and resid 109 through 214)FF109 - 214109 - 214

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