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- PDB-8xwz: Non-crystalline proximal tubulopathy and crystalline cast nephrop... -

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Basic information

Entry
Database: PDB / ID: 8xwz
TitleNon-crystalline proximal tubulopathy and crystalline cast nephropathy-causing Bence-Jones protein PT-CN: An entire immunoglobulin kappa light chain dimer
ComponentsBence-Jones protein kappa light chain PT-CN
KeywordsIMMUNE SYSTEM / Bence-Jones protein / immunoglobulin / kappa light chain
Function / homology2-ETHOXYETHANOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsEzawa, T. / Otomo, R. / Nozawa, K. / Kyoya, S. / Noguchi, K. / Yohda, M. / Odaka, M. / Matsumura, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K07011 Japan
Japan Society for the Promotion of Science (JSPS)23KJ0224 Japan
CitationJournal: Faseb J. / Year: 2025
Title: Multiple myeloma-associated non-crystalline proximal tubulopathy and crystalline cast nephropathy: Biochemical and structural features of disease-causing monoclonal kappa light chains.
Authors: Ezawa, T. / Otomo, R. / Kariya, Y. / Nozawa, K. / Kyoya, S. / Furutani, C. / Noguchi, K. / Yohda, M. / Odaka, M. / Matsumura, H. / Saito, A. / Saito, M. / Abe, F. / Fujioka, Y. / Kitadate, A. ...Authors: Ezawa, T. / Otomo, R. / Kariya, Y. / Nozawa, K. / Kyoya, S. / Furutani, C. / Noguchi, K. / Yohda, M. / Odaka, M. / Matsumura, H. / Saito, A. / Saito, M. / Abe, F. / Fujioka, Y. / Kitadate, A. / Wakui, H. / Takahashi, N.
History
DepositionJan 17, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bence-Jones protein kappa light chain PT-CN
B: Bence-Jones protein kappa light chain PT-CN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,90381
Polymers46,6042
Non-polymers5,29979
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.422, 80.422, 141.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-301-

PO4

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Components

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Antibody , 1 types, 2 molecules AB

#1: Antibody Bence-Jones protein kappa light chain PT-CN


Mass: 23301.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: DDBJ:LC795522 / Source: (natural) Homo sapiens (human)

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Non-polymers , 7 types, 198 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ETX / 2-ETHOXYETHANOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 69 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 283 K / Method: counter-diffusion / pH: 6.5 / Details: 100 mM HEPES, 8% MPD, 10% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.04 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 6, 2022
RadiationMonochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.3→47.08 Å / Num. obs: 21369 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 45.92 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2051 / CC1/2: 0.591 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B6D

1b6d


Resolution: 2.3→44.29 Å / SU ML: 0.2938 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 25.4893 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2567 1079 5.06 %
Rwork0.2044 20231 -
obs0.2071 21310 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.02 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3255 0 338 119 3712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213612
X-RAY DIFFRACTIONf_angle_d0.5594757
X-RAY DIFFRACTIONf_chiral_restr0.0404518
X-RAY DIFFRACTIONf_plane_restr0.0026586
X-RAY DIFFRACTIONf_dihedral_angle_d7.00812849
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40.33931190.28282476X-RAY DIFFRACTION100
2.4-2.530.28911250.25872488X-RAY DIFFRACTION100
2.53-2.690.32981510.24292462X-RAY DIFFRACTION100
2.69-2.90.28731420.22652480X-RAY DIFFRACTION100
2.9-3.190.25961040.20942548X-RAY DIFFRACTION100
3.19-3.650.26131510.18462495X-RAY DIFFRACTION100
3.65-4.60.22371350.16542569X-RAY DIFFRACTION100
4.6-44.290.23951520.21342713X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -11.1897755859 Å / Origin y: 31.947557266 Å / Origin z: -13.3652717263 Å
111213212223313233
T0.280500188068 Å2-0.0128068544455 Å2-0.0710490553213 Å2-0.300710649078 Å2-0.0303731384168 Å2--0.227806983348 Å2
L1.6271375089 °2-0.689154268978 °2-1.07045312687 °2-1.51543080886 °20.723603630138 °2--0.864508056649 °2
S-0.0335829495335 Å °-0.053428664978 Å °0.0332668237067 Å °0.00607692303231 Å °0.002681441324 Å °0.0695171425978 Å °-0.14597653236 Å °0.0899179954992 Å °0.0349331015563 Å °
Refinement TLS groupSelection details: all

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