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- PDB-9gff: BCR Fab from the subset 1 chronic lymphocytic leukaemia case P10015 -

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Basic information

Entry
Database: PDB / ID: 9gff
TitleBCR Fab from the subset 1 chronic lymphocytic leukaemia case P10015
Components
  • BCR P10015 heavy chain
  • BCR P10015 light chain
KeywordsIMMUNE SYSTEM / B-cell receptor / Fab / chronicl lymphocytic leukaemia
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMinici, C. / Degano, M.
Funding support Italy, United Kingdom, 4items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchIG25764 Italy
Italian Association for Cancer ResearchIG17032 Italy
Worldwide Cancer Research19-0096 United Kingdom
Italian Ministry of HealthRF-2018-12368231 Italy
CitationJournal: Nat Commun / Year: 2025
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. / Gounari, M. / Linder, A.T. / Akpinaroglu, C. / Patrone, M. / Broggini, L. / Frenquelli, M. / Sarrigeorgiou, I. / Lymberi, P. / Petrakis, G. / ...Authors: Cocomazzi, P.G. / Iatrou, A. / Minici, C. / Gounari, M. / Linder, A.T. / Akpinaroglu, C. / Patrone, M. / Broggini, L. / Frenquelli, M. / Sarrigeorgiou, I. / Lymberi, P. / Petrakis, G. / Koletsa, T. / Scarfo, L. / Agathangelidis, A. / Jumaa, H. / Maity, P.C. / Ghia, P. / Stamatopoulos, K. / Degano, M.
History
DepositionAug 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: BCR P10015 heavy chain
L: BCR P10015 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5933
Polymers48,0232
Non-polymers5711
Water36020
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.952, 99.952, 123.048
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c

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Components

#1: Antibody BCR P10015 heavy chain


Mass: 24538.531 Da / Num. of mol.: 1
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: Antibody BCR P10015 light chain


Mass: 23484.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
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: 3.69 Å3/Da / Density % sol: 66.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M ammonium succinate pH 7 and 1.5 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.51→86.57 Å / Num. obs: 23294 / % possible obs: 99.8 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rpim(I) all: 0.043 / Net I/σ(I): 14
Reflection shellResolution: 2.51→2.64 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2319 / CC1/2: 0.465 / Rpim(I) all: 0.746 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SCALAdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→86.56 Å / SU ML: 0.3214 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.5545
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2348 796 4.62 %RANDOM
Rwork0.2088 16432 --
obs0.21 17228 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.83 Å2
Refinement stepCycle: LAST / Resolution: 2.8→86.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 0 38 20 3424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00443489
X-RAY DIFFRACTIONf_angle_d0.69464747
X-RAY DIFFRACTIONf_chiral_restr0.047536
X-RAY DIFFRACTIONf_plane_restr0.0041606
X-RAY DIFFRACTIONf_dihedral_angle_d13.33611265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.970.36971190.35172732X-RAY DIFFRACTION99.72
2.97-3.20.27621340.30042722X-RAY DIFFRACTION99.83
3.2-3.530.2691410.26282726X-RAY DIFFRACTION100
3.53-4.040.25321350.23382722X-RAY DIFFRACTION99.97
4.04-5.090.17731530.16762732X-RAY DIFFRACTION99.97
5.09-86.560.24181140.17492798X-RAY DIFFRACTION99.93
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)
12.462707460760.265245112835-0.07366982119665.504832795712.050130735485.702752903580.02558964827170.280341266150.0320082112085-0.189669884693-0.0824905820277-0.274976812175-0.1473741368010.901483048078-0.01724495696950.417369859816-0.005685068750890.04993546352770.8245799968830.04842169264280.458496195389-22.2691490761-34.4678382936-12.397509898
22.10629834221-0.196788409272-0.5400964149563.17575361276-1.775793350494.4607106934-0.051352321726-0.0282714611781-0.1507505112190.284683399962-0.263821405451-0.45559762415-0.4239740845541.078963401120.3032831325620.660289068461-0.120733304098-0.1263943824181.148875465450.07079057182690.756641135128-17.2079499246-31.649099707220.5970272565
32.832148233680.09093828652210.002817823151173.377172879470.6890391894666.922367933660.0129421698208-0.126435244362-0.08928342394560.236088916069-0.2439441041430.2495520704880.3378257046380.1230695526280.2409586298130.494350147171-0.007299784783680.07726681614650.465104311075-0.002169702311710.546839871795-41.4603417624-41.0460680638-4.0856219434
44.784494312091.05159131022-1.202250416422.6005696890.844445342982.42974100272-0.142225291145-0.5860423658460.4635628878540.1727050539440.000559572620537-0.388860785892-0.7371723795850.4790510353020.2012418412850.833150711461-0.065043869622-0.2277902346260.8593029811990.1045429525150.587155439324-28.7046440745-21.267316168925.7789825893
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 1 through 118 )HA1 - 1181 - 118
22chain 'H' and (resid 119 through 224)HA - D119 - 224119
33chain 'L' and (resid 1 through 109 )LE1 - 1091 - 109
44chain 'L' and (resid 110 through 214 )LE110 - 214110 - 214

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