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- PDB-7wki: Structure of the ultra-affinity complex between CFH and a nanobody -

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Basic information

Entry
Database: PDB / ID: 7wki
TitleStructure of the ultra-affinity complex between CFH and a nanobody
Components
  • Anti-CFH nanobody (VHH)
  • Complement factor H
KeywordsIMMUNE SYSTEM / Ultra-high affinity / Nanobody / Atypical Hemolytic Uremic Syndrome / Complement system / autoantibody / autoimmune disease
Function / homology
Function and homology information


regulation of complement activation, alternative pathway / symbiont cell surface / regulation of complement-dependent cytotoxicity / regulation of complement activation / complement component C3b binding / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation / complement activation, alternative pathway / Regulation of Complement cascade ...regulation of complement activation, alternative pathway / symbiont cell surface / regulation of complement-dependent cytotoxicity / regulation of complement activation / complement component C3b binding / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation / complement activation, alternative pathway / Regulation of Complement cascade / heparin binding / blood microparticle / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
: / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCaaveiro, J.M.M. / Yokoo, T. / Tsumoto, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Antibody recognition of complement factor H reveals a flexible loop involved in atypical hemolytic uremic syndrome pathogenesis.
Authors: Yokoo, T. / Tanabe, A. / Yoshida, Y. / Caaveiro, J.M.M. / Nakakido, M. / Ikeda, Y. / Fujimura, Y. / Matsumoto, M. / Entzminger, K. / Maruyama, T. / Okumura, C.J. / Nangaku, M. / Tsumoto, K.
History
DepositionJan 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 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: Complement factor H
B: Anti-CFH nanobody (VHH)


Theoretical massNumber of molelcules
Total (without water)37,1602
Polymers37,1602
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-9 kcal/mol
Surface area14270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.960, 75.960, 143.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Complement factor H / H factor 1


Mass: 22124.023 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFH, HF, HF1, HF2 / Cell line (production host): EXPI293 / Production host: Homo sapiens (human) / References: UniProt: P08603
#2: Antibody Anti-CFH nanobody (VHH)


Mass: 15036.458 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) / Strain (production host): BL1-23 / Variant (production host): DE3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.21 Å3/Da / Density % sol: 61.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Sodium Phosphate monohydrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→48.44 Å / Num. obs: 15303 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.16 / Net I/σ(I): 12.3
Reflection shellResolution: 2.6→2.74 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2204 / CC1/2: 0.916

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
MOSFLM7.2.2data reduction
SCALA3.3.22data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SW0, 5LHN

3sw0

5lhn


Resolution: 2.6→48.44 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 22.748 / SU ML: 0.208 / Cross valid method: FREE R-VALUE / ESU R: 0.284 / ESU R Free: 0.236
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2392 753 4.928 %
Rwork0.1921 14528 -
all0.194 --
obs-15281 99.876 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 62.83 Å2
Baniso -1Baniso -2Baniso -3
1-1.925 Å20.962 Å20 Å2
2--1.925 Å20 Å2
3----6.245 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1985 0 0 25 2010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132044
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171809
X-RAY DIFFRACTIONr_angle_refined_deg1.8631.6512777
X-RAY DIFFRACTIONr_angle_other_deg1.3451.5754217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6895259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.98721.584101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.40215327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.31514
X-RAY DIFFRACTIONr_chiral_restr0.0740.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022313
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02441
X-RAY DIFFRACTIONr_nbd_refined0.2120.2330
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.21641
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2951
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21041
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0920.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1580.29
X-RAY DIFFRACTIONr_nbd_other0.1970.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2240.26
X-RAY DIFFRACTIONr_mcbond_it2.825.0771036
X-RAY DIFFRACTIONr_mcbond_other2.795.0761035
X-RAY DIFFRACTIONr_mcangle_it4.3457.6071292
X-RAY DIFFRACTIONr_mcangle_other4.3497.611293
X-RAY DIFFRACTIONr_scbond_it3.6235.4641008
X-RAY DIFFRACTIONr_scbond_other3.6225.4641008
X-RAY DIFFRACTIONr_scangle_it5.5728.0241484
X-RAY DIFFRACTIONr_scangle_other5.5718.0261485
X-RAY DIFFRACTIONr_lrange_it7.15456.2162134
X-RAY DIFFRACTIONr_lrange_other7.15256.2282134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6680.394510.351053X-RAY DIFFRACTION99.5491
2.668-2.7410.351500.3011046X-RAY DIFFRACTION99.8178
2.741-2.820.304600.282974X-RAY DIFFRACTION99.7107
2.82-2.9060.304610.285957X-RAY DIFFRACTION100
2.906-3.0020.321380.251966X-RAY DIFFRACTION99.9005
3.002-3.1070.262510.235885X-RAY DIFFRACTION100
3.107-3.2240.262500.23884X-RAY DIFFRACTION99.893
3.224-3.3550.331580.226843X-RAY DIFFRACTION100
3.355-3.5040.189380.194815X-RAY DIFFRACTION99.8829
3.504-3.6740.206260.192812X-RAY DIFFRACTION100
3.674-3.8720.247470.188741X-RAY DIFFRACTION100
3.872-4.1060.249390.158703X-RAY DIFFRACTION99.8654
4.106-4.3890.181290.145672X-RAY DIFFRACTION99.8576
4.389-4.7380.145270.121651X-RAY DIFFRACTION100
4.738-5.1880.229250.132566X-RAY DIFFRACTION100
5.188-5.7960.258270.147544X-RAY DIFFRACTION100
5.796-6.6840.185300.159471X-RAY DIFFRACTION100
6.684-8.1650.19260.156401X-RAY DIFFRACTION100
8.165-11.4590.256130.163334X-RAY DIFFRACTION100
11.459-48.440.2670.333210X-RAY DIFFRACTION98.6364
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)
13.9466-1.81493.54171.8505-2.10024.72180.21260.2545-0.2356-0.227-0.06050.1680.28250.0639-0.15210.1250.00980.02980.0839-0.0270.0489-47.162818.402-1.8533
21.6379-1.13850.3093.55430.60195.67030.0279-0.1731-0.08540.09680.0635-0.2470.03120.275-0.09140.00840.0025-0.01580.06160.01220.0392-32.304417.345730.9922
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1105 - 1231
2X-RAY DIFFRACTION2ALLB2 - 133

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