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- PDB-5gkr: Crystal structure of SLE patient-derived anti-DNA antibody in com... -

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Basic information

Entry
Database: PDB / ID: 5gkr
TitleCrystal structure of SLE patient-derived anti-DNA antibody in complex with oligonucleotide
Components
  • DNA (5'-D(P*TP*TP*TP*T)-3')
  • IgG2, Fab (heavy chain)
  • lambda, Fab (light chain)
KeywordsIMMUNE SYSTEM/DNA / antibody / lupus / DNA / Fab / IMMUNE SYSTEM-DNA complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsArimori, T. / Sakakibara, S. / Kikutani, H. / Takagi, J.
CitationJournal: Sci Rep / Year: 2017
Title: Clonal evolution and antigen recognition of anti-nuclear antibodies in acute systemic lupus erythematosus
Authors: Sakakibara, S. / Arimori, T. / Yamashita, K. / Jinzai, H. / Motooka, D. / Nakamura, S. / Li, S. / Takeda, K. / Katayama, J. / El Hussien, M.A. / Narazaki, M. / Tanaka, T. / Standley, D.M. / ...Authors: Sakakibara, S. / Arimori, T. / Yamashita, K. / Jinzai, H. / Motooka, D. / Nakamura, S. / Li, S. / Takeda, K. / Katayama, J. / El Hussien, M.A. / Narazaki, M. / Tanaka, T. / Standley, D.M. / Takagi, J. / Kikutani, H.
History
DepositionJul 5, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IgG2, Fab (heavy chain)
B: lambda, Fab (light chain)
C: IgG2, Fab (heavy chain)
D: lambda, Fab (light chain)
T: DNA (5'-D(P*TP*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)93,8635
Polymers93,8635
Non-polymers00
Water2,810156
1
A: IgG2, Fab (heavy chain)
B: lambda, Fab (light chain)
T: DNA (5'-D(P*TP*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)47,5173
Polymers47,5173
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: IgG2, Fab (heavy chain)
D: lambda, Fab (light chain)


Theoretical massNumber of molelcules
Total (without water)46,3462
Polymers46,3462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-24 kcal/mol
Surface area18830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.515, 147.515, 112.807
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A2 - 215
2010C2 - 215
1020B3 - 212
2020D3 - 212

NCS ensembles :
ID
1
2

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Components

#1: Antibody IgG2, Fab (heavy chain)


Mass: 23397.178 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody lambda, Fab (light chain)


Mass: 22948.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*TP*TP*TP*T)-3')


Mass: 1171.814 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl (pH 7.0), 0.2 M NaCl, 1 M Sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.67
11K, H, -L20.33
ReflectionResolution: 2.1→50 Å / Num. obs: 53509 / % possible obs: 100 % / Redundancy: 5.8 % / Rsym value: 0.115 / Net I/σ(I): 23.1
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.857 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QHK, 4Y5Y, 4IDJ, and 4LLW

4qhk

4y5y

4idj

4llw


Resolution: 2.1→26.33 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.593 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.03 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18512 2609 4.9 %RANDOM
Rwork0.16253 ---
obs0.16359 50879 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.752 Å2
Baniso -1Baniso -2Baniso -3
1--2.08 Å2-0 Å2-0 Å2
2---2.08 Å2-0 Å2
3---4.16 Å2
Refinement stepCycle: 1 / Resolution: 2.1→26.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6239 64 0 156 6459
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196478
X-RAY DIFFRACTIONr_bond_other_d0.0030.025853
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.9388855
X-RAY DIFFRACTIONr_angle_other_deg1.051313575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6465819
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.26824.097227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36915968
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9161517
X-RAY DIFFRACTIONr_chiral_restr0.0750.21003
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217225
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021416
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5452.2813303
X-RAY DIFFRACTIONr_mcbond_other0.5452.2813302
X-RAY DIFFRACTIONr_mcangle_it0.9613.4144113
X-RAY DIFFRACTIONr_mcangle_other0.9613.4144114
X-RAY DIFFRACTIONr_scbond_it0.5152.3663175
X-RAY DIFFRACTIONr_scbond_other0.5082.3643171
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8823.5294740
X-RAY DIFFRACTIONr_long_range_B_refined2.92718.1536698
X-RAY DIFFRACTIONr_long_range_B_other2.92718.1516697
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A208400.11
12C208400.11
21B209060.1
22D209060.1
LS refinement shellResolution: 2.099→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 176 -
Rwork0.203 3756 -
obs--99.75 %
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)
11.08190.118-0.01771.1930.35851.5858-0.0290.01510.02870.00290.0422-0.0508-0.04030.0258-0.01320.12730.00180.00210.16490.00260.0114-35.597135.1141.257
21.71930.1505-0.12960.5354-0.08451.58290.026-0.01310.00080.06320.0191-0.0273-0.0023-0.0586-0.04510.16220.0002-0.02720.1479-0.01490.0162-34.615133.68222.775
32.12010.16781.37083.04550.91253.48390.17180.1665-0.26580.2682-0.0875-0.03340.69250.1657-0.08430.26650.06250.00470.1618-0.06220.05475.788111.37228.996
42.9045-1.32331.56642.3881-1.14963.04150.25950.4894-0.1998-0.1445-0.21040.1340.57790.2754-0.04910.28070.0604-0.00870.3353-0.15420.0804-2.567114.3919.437
52.40580.9305-0.80222.1838-0.86311.3029-0.0469-0.12430.0386-0.0171-0.0488-0.0121-0.10980.02450.09560.1258-0.0678-0.0140.1609-0.03640.0222-62.393112.3289.109
60.90561.07320.56616.05583.54063.81670.14540.0814-0.25950.49270.16-0.41430.24080.2356-0.30540.1089-0.016-0.06990.1976-0.0090.0896-48.821108.1318.056
71.8174-0.33820.18622.2246-0.71212.1351-0.03330.24480.0986-0.05860.03080.0417-0.0747-0.04170.00240.0887-0.0585-0.0130.1746-00.01963.258146.92628.179
85.40323.96020.88494.10440.69463.2454-0.36590.5756-0.0498-0.51140.4662-0.1189-0.02980.1019-0.10020.1184-0.07850.02510.2539-0.03310.01210.184142.64113.695
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 116
2X-RAY DIFFRACTION2B2 - 110
3X-RAY DIFFRACTION3C2 - 116
4X-RAY DIFFRACTION4D3 - 108
5X-RAY DIFFRACTION5A117 - 212
6X-RAY DIFFRACTION6B111 - 210
7X-RAY DIFFRACTION7C117 - 213
8X-RAY DIFFRACTION8D113 - 209

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