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- PDB-9gfg: BCR Fab from the subset 1 chronic lymphocytic leukaemia case P3129 -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9gfg
TitleBCR Fab from the subset 1 chronic lymphocytic leukaemia case P3129
Components
  • BCR P3129 heavy chain
  • BCR P3129 light chain
KeywordsIMMUNE SYSTEM / BCR / Fab / chronic lymphocytic leukaemia
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMinici, C. / Degano, M.
Funding support Italy, United Kingdom, 4items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchIG17032 Italy
Italian Association for Cancer ResearchIG25764 Italy
Worldwide Cancer Research19-0096 United Kingdom
Italian Ministry of HealthRF-2018-12368231 Italy
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
H: BCR P3129 heavy chain
L: BCR P3129 light chain
A: BCR P3129 heavy chain
B: BCR P3129 light chain
C: BCR P3129 heavy chain
D: BCR P3129 light chain
E: BCR P3129 heavy chain
F: BCR P3129 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,22625
Polymers192,0708
Non-polymers2,15617
Water2,900161
1
H: BCR P3129 heavy chain
L: BCR P3129 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8107
Polymers48,0172
Non-polymers7935
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: BCR P3129 heavy chain
B: BCR P3129 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6077
Polymers48,0172
Non-polymers5905
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: BCR P3129 heavy chain
D: BCR P3129 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5156
Polymers48,0172
Non-polymers4974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: BCR P3129 heavy chain
F: BCR P3129 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2945
Polymers48,0172
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.696, 87.891, 115.528
Angle α, β, γ (deg.)90.000, 94.590, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 80 or resid 82...
d_2ens_1(chain "C" and (resid 2 through 80 or resid 82...
d_3ens_1(chain "E" and (resid 2 through 80 or resid 82...
d_4ens_1(chain "H" and (resid 2 through 80 or resid 82...
d_1ens_2(chain "B" and (resid 1 through 82 or resid 84...
d_2ens_2(chain "D" and (resid 1 through 82 or resid 84...
d_3ens_2(chain "F" and (resid 1 through 82 or resid 84...
d_4ens_2(chain "L" and (resid 1 through 82 or resid 84...

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_1VALVALTYRTYRAC2 - 802 - 80
d_12ens_1GLUGLUSERSERAC82 - 13382 - 133
d_13ens_1SERSERLYSLYSAC143 - 165143 - 165
d_14ens_1SERSERALAALAAC172 - 187172 - 187
d_15ens_1SERSERSERSERAC189 - 195189 - 195
d_16ens_1VALVALLEULEUAC207 - 223207 - 223
d_21ens_1VALVALTYRTYRCE2 - 802 - 80
d_22ens_1GLUGLUSERSERCE82 - 13382 - 133
d_23ens_1SERSERLYSLYSCE143 - 165143 - 165
d_24ens_1SERSERALAALACE172 - 187172 - 187
d_25ens_1SERSERSERSERCE189 - 195189 - 195
d_26ens_1VALVALLEULEUCE207 - 223207 - 223
d_31ens_1VALVALTYRTYREG2 - 802 - 80
d_32ens_1GLUGLUALAALAEG82 - 18782 - 187
d_33ens_1SERSERSERSEREG189 - 195189 - 195
d_34ens_1VALVALLEULEUEG207 - 223207 - 223
d_41ens_1VALVALTYRTYRHA2 - 802 - 80
d_42ens_1GLUGLUSERSERHA82 - 13382 - 133
d_43ens_1SERSERLYSLYSHA143 - 165143 - 165
d_44ens_1SERSERALAALAHA172 - 187172 - 187
d_45ens_1SERSERSERSERHA189 - 195189 - 195
d_46ens_1VALVALLEULEUHA207 - 223207 - 223
d_11ens_2ASPASPASPASPBD1 - 821 - 82
d_12ens_2ALAALAGLNGLNBD84 - 9084 - 90
d_13ens_2TYRTYRLYSLYSBD92 - 10492 - 104
d_14ens_2GLUGLUVALVALBD106 - 164106 - 164
d_15ens_2GLUGLUARGARGBD166 - 212166 - 212
d_21ens_2ASPASPASPASPDF1 - 821 - 82
d_22ens_2ALAALAGLNGLNDF84 - 9084 - 90
d_23ens_2TYRTYRLYSLYSDF92 - 10492 - 104
d_24ens_2GLUGLUVALVALDF106 - 164106 - 164
d_25ens_2GLUGLUARGARGDF166 - 212166 - 212
d_31ens_2ASPASPASPASPFH1 - 821 - 82
d_32ens_2ALAALAGLNGLNFH84 - 9084 - 90
d_33ens_2TYRTYRLYSLYSFH92 - 10492 - 104
d_34ens_2GLUGLUVALVALFH106 - 164106 - 164
d_35ens_2GLUGLUARGARGFH166 - 212166 - 212
d_41ens_2ASPASPASPASPLB1 - 821 - 82
d_42ens_2ALAALAGLNGLNLB84 - 9084 - 90
d_43ens_2TYRTYRLYSLYSLB92 - 10492 - 104
d_44ens_2GLUGLUVALVALLB106 - 164106 - 164
d_45ens_2GLUGLUARGARGLB166 - 212166 - 212

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.69288676591, 0.563031252797, 0.450448374402), (0.566413713773, 0.0384357570902, 0.823224269216), (0.446187667329, 0.825541338124, -0.345540250292)-37.7466022506, 2.90112301011, 23.1804994388
2given(0.675180058811, -0.529241834879, -0.513843330596), (0.62099106346, 0.031845296071, 0.783170464344), (-0.398123080576, -0.847873196493, 0.350155758743)10.8214747795, 5.15024021308, -26.4423479128
3given(-0.981799780213, -0.169275095608, -0.0861111698977), (-0.17254445107, 0.984481679529, 0.0320036728639), (0.0793574443833, 0.0462792035248, -0.995771375036)-22.5246282363, -2.90020703468, -2.77334863265
4given(-0.671806965786, 0.558651728489, 0.486398650263), (0.571370231647, -0.0270583000239, 0.820246247652), (0.471393104648, 0.828960852306, -0.301019013079)-38.7262231344, 3.7591977189, 22.3353461291
5given(0.654051355956, -0.525705792705, -0.543921173783), (0.638104772111, -0.00273143808501, 0.7699446987), (-0.406250075178, -0.850662070838, 0.333668874268)11.3027156276, 6.46621984037, -25.9744819724
6given(-0.97130713528, -0.188730237274, -0.144718162277), (-0.188350737641, 0.981964132483, -0.0164451253019), (0.145211737076, 0.0112845050687, -0.989336247876)-18.8804529904, -1.65002433749, -1.11379448766

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Components

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Antibody , 2 types, 8 molecules HACELBDF

#1: Antibody
BCR P3129 heavy chain


Mass: 24574.498 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: Antibody
BCR P3129 light chain


Mass: 23442.932 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, 3 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: 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.: 2 / 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, 175 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M sodium potassium tartrate pH 7, 0.1 M magnesium chloride, 20% PEG 3,350

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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: 2.11→115.2 Å / Num. obs: 120564 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rpim(I) all: 0.032 / Net I/σ(I): 10
Reflection shellResolution: 2.11→2.16 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 8714 / CC1/2: 0.238 / Rpim(I) all: 0.83 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→80.6 Å / SU ML: 0.3417 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.5007
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2464 4549 4.9 %RANDOM
Rwork0.2201 88350 --
obs0.2214 92899 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.74 Å2
Refinement stepCycle: LAST / Resolution: 2.3→80.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13013 0 140 161 13314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313472
X-RAY DIFFRACTIONf_angle_d0.633718279
X-RAY DIFFRACTIONf_chiral_restr0.04632040
X-RAY DIFFRACTIONf_plane_restr0.00442322
X-RAY DIFFRACTIONf_dihedral_angle_d12.67154862
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CAX-RAY DIFFRACTIONTorsion NCS1.42537196691
ens_1d_3CAX-RAY DIFFRACTIONTorsion NCS1.13234286618
ens_1d_4CAX-RAY DIFFRACTIONTorsion NCS2.00160961119
ens_2d_2DBX-RAY DIFFRACTIONTorsion NCS1.17382468308
ens_2d_3DBX-RAY DIFFRACTIONTorsion NCS1.01395738255
ens_2d_4DBX-RAY DIFFRACTIONTorsion NCS1.93565574676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.46091310.39662840X-RAY DIFFRACTION96.84
2.33-2.350.3711300.38062984X-RAY DIFFRACTION99.97
2.35-2.380.3911500.36462947X-RAY DIFFRACTION99.9
2.38-2.410.41941440.36872890X-RAY DIFFRACTION99.93
2.41-2.440.35991470.35892971X-RAY DIFFRACTION99.97
2.44-2.480.41421410.35932912X-RAY DIFFRACTION99.87
2.48-2.510.41511450.34172955X-RAY DIFFRACTION99.87
2.51-2.550.34941670.35532927X-RAY DIFFRACTION99.74
2.55-2.590.38811330.36862950X-RAY DIFFRACTION99.97
2.59-2.630.37751520.34762932X-RAY DIFFRACTION99.94
2.63-2.680.31371580.30832933X-RAY DIFFRACTION100
2.68-2.730.3131870.29132881X-RAY DIFFRACTION99.93
2.73-2.780.34441460.28482929X-RAY DIFFRACTION100
2.78-2.830.28931580.25893001X-RAY DIFFRACTION100
2.83-2.90.2721450.25682898X-RAY DIFFRACTION99.93
2.9-2.960.29461490.25732966X-RAY DIFFRACTION100
2.96-3.040.29361460.26832955X-RAY DIFFRACTION99.94
3.04-3.120.29691730.27762904X-RAY DIFFRACTION99.94
3.12-3.210.33111540.28292931X-RAY DIFFRACTION99.97
3.21-3.320.28681590.25452934X-RAY DIFFRACTION99.94
3.32-3.430.24961420.22622959X-RAY DIFFRACTION99.87
3.43-3.570.22171430.21852955X-RAY DIFFRACTION99.77
3.57-3.730.23891560.21342970X-RAY DIFFRACTION99.81
3.73-3.930.25121680.21722930X-RAY DIFFRACTION99.77
3.93-4.180.20441410.18962976X-RAY DIFFRACTION100
4.18-4.50.18491570.16082957X-RAY DIFFRACTION100
4.5-4.950.16511380.15252980X-RAY DIFFRACTION99.84
4.95-5.670.21391690.16382952X-RAY DIFFRACTION99.81
5.67-7.140.211840.19892952X-RAY DIFFRACTION99.33
7.14-80.60.22351360.19063079X-RAY DIFFRACTION99.41
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)
14.34266226161-0.0164827286705-2.440114225430.799463440521-0.0008952725168553.024176371190.1537156599880.299782830690.0814593181983-0.1372657159750.00125876057109-0.0780277412256-0.00746418126365-0.160535596695-0.1465400183660.777102384902-0.0045399988411-0.04254114307070.3109975690970.03158941337430.4311422282455.9826961635922.3354770195-47.001403505
23.007782876620.247822682849-0.07397383901431.036965700550.08991318488160.9385119754210.0155699009793-0.265488807732-0.3234360205990.0345881024298-0.00480128649238-0.2594254531560.468876828385-0.0141348944478-0.00233944736290.842313087770.0129339207336-0.0962791629670.3778295359650.03135891896470.4654782016928.749396193194.53771539406-45.9638468621
33.533281995321.20997256484-0.8966167323251.55759061874-0.5475543006171.639429108660.290038849785-0.1033437607140.2208119179170.158436199266-0.1983856209510.268912932363-0.449593676041-0.186744514204-0.1191011558670.8165151221820.07120478622430.03300930094720.392283049586-0.05255121580830.492380868627-36.212623658317.792707666942.3461962586
43.450327199870.437728062456-0.08759164986450.75204663575-0.156177626980.664393254240.1249563607020.264837727347-0.17683643447-0.142012939838-0.06515530074710.0580756022009-0.0147941554603-0.207789539463-0.0705211160320.757516184637-0.0191434261329-0.008624090885970.512924660979-0.03050004705950.472921066566-34.6075873430.33102437634440.3012605534
53.55178117854-0.755978590496-3.199040065832.000574931450.4796482734133.56073996777-0.0321680737085-0.902795863975-0.1951271073130.439363033312-0.087572805236-0.635801578289-0.3467896775540.7874670432360.1272644519540.677286329794-0.117530802515-0.2727842309470.8543384036610.2255230568590.80602535161815.490722843417.53591316948.72113443314
61.26928771173-1.0089185874-0.2888607838423.76159874006-0.8931309755873.050345660440.07885260168440.01015329912570.0340514501323-0.466386135603-0.0095636841131-0.1621805323110.119328749315-0.181884959035-0.07781223442270.569787086534-0.109745949727-0.07300201251850.5018359086890.02737397396780.3844529934224.2399272446317.0463791212-5.79330332331
70.741810901497-0.720692959748-1.265575899140.4966212253370.6322078041073.41129416228-0.1491547934230.23683270731-0.1966092076850.0193793176772-0.02227548124170.4803502143490.783980738188-1.143522122220.1546284415860.735909844715-0.414742120915-0.1577021641611.182439397720.1195393190730.7776851286-43.066724061116.0462851758-14.780701261
80.9976660960560.0174145355732-1.194667122661.54583219474-0.5689446707333.27934032057-0.185060503580.128123930793-0.09967362690.3081078847810.2765820950170.3698068919020.741829842312-0.202318751772-0.104624613540.772307882582-0.141054966221-0.00401488457960.6915627405590.05455983876080.585967079073-33.165489954215.59310921231.05759088062
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 225)HA - B1 - 2251
22(chain 'L' and resid 1 through 214)LD1 - 2141 - 214
33(chain 'A' and resid 1 through 301)AE - F1 - 3011
44(chain 'B' and resid 1 through 215)BG1 - 2151 - 215
55(chain 'C' and resid 2 through 301)CH - I2 - 3011
66(chain 'D' and resid 1 through 214)DJ1 - 2141 - 214
77(chain 'E' and resid 1 through 301)EK1 - 2231 - 200
88(chain 'F' and resid 1 through 212)FL1 - 2121 - 212

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