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- PDB-5b71: Crystal structure of complement C5 in complex with SKY59 -

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Basic information

Entry
Database: PDB / ID: 5b71
TitleCrystal structure of complement C5 in complex with SKY59
Components
  • Complement C5 beta chain
  • SKY59 Fab heavy chain
  • SKY59 Fab light chain
KeywordsIMMUNE SYSTEM / pH-dependent / recycling antibody / complement C5 / Fab / Complex
Function / homology
Function and homology information


Terminal pathway of complement / membrane attack complex / negative regulation of macrophage chemotaxis / Activation of C3 and C5 / complement activation, GZMK pathway / other organism cell membrane / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production ...Terminal pathway of complement / membrane attack complex / negative regulation of macrophage chemotaxis / Activation of C3 and C5 / complement activation, GZMK pathway / other organism cell membrane / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / positive regulation of chemokine production / Regulation of Complement cascade / Peptide ligand-binding receptors / chemotaxis / killing of cells of another organism / G alpha (i) signalling events / cell surface receptor signaling pathway / inflammatory response / G protein-coupled receptor signaling pathway / signaling receptor binding / : / extracellular exosome / extracellular region
Similarity search - Function
Macroglobulin (MG2) domain / : / Complement component 5, CUB domain / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain ...Macroglobulin (MG2) domain / : / Complement component 5, CUB domain / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Macroglobulin domain MG4 / Macroglobulin domain MG4 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Tissue inhibitor of metalloproteinases-like, OB-fold / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.11 Å
AuthorsIrie, M. / Shimizu, Y. / Sampei, Z. / Fukuzawa, T.
CitationJournal: Sci Rep / Year: 2017
Title: Long lasting neutralization of C5 by SKY59, a novel recycling antibody, is a potential therapy for complement-mediated diseases.
Authors: Fukuzawa, T. / Sampei, Z. / Haraya, K. / Ruike, Y. / Shida-Kawazoe, M. / Shimizu, Y. / Gan, S.W. / Irie, M. / Tsuboi, Y. / Tai, H. / Sakiyama, T. / Sakamoto, A. / Ishii, S. / Maeda, A. / ...Authors: Fukuzawa, T. / Sampei, Z. / Haraya, K. / Ruike, Y. / Shida-Kawazoe, M. / Shimizu, Y. / Gan, S.W. / Irie, M. / Tsuboi, Y. / Tai, H. / Sakiyama, T. / Sakamoto, A. / Ishii, S. / Maeda, A. / Iwayanagi, Y. / Shibahara, N. / Shibuya, M. / Nakamura, G. / Nambu, T. / Hayasaka, A. / Mimoto, F. / Okura, Y. / Hori, Y. / Habu, K. / Wada, M. / Miura, T. / Tachibana, T. / Honda, K. / Tsunoda, H. / Kitazawa, T. / Kawabe, Y. / Igawa, T. / Hattori, K. / Nezu, J.
History
DepositionJun 3, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 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 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SKY59 Fab light chain
B: SKY59 Fab heavy chain
C: SKY59 Fab light chain
D: SKY59 Fab heavy chain
E: Complement C5 beta chain
F: Complement C5 beta chain


Theoretical massNumber of molelcules
Total (without water)119,4956
Polymers119,4956
Non-polymers00
Water5,801322
1
A: SKY59 Fab light chain
B: SKY59 Fab heavy chain
E: Complement C5 beta chain


Theoretical massNumber of molelcules
Total (without water)59,7483
Polymers59,7483
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-28 kcal/mol
Surface area23950 Å2
MethodPISA
2
C: SKY59 Fab light chain
D: SKY59 Fab heavy chain
F: Complement C5 beta chain


Theoretical massNumber of molelcules
Total (without water)59,7483
Polymers59,7483
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-31 kcal/mol
Surface area23430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.790, 55.100, 127.760
Angle α, β, γ (deg.)89.180, 86.240, 78.200
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody SKY59 Fab light chain


Mass: 23328.748 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#2: Antibody SKY59 Fab heavy chain


Mass: 24121.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Protein Complement C5 beta chain


Mass: 12297.792 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 20-124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C5, CPAMD4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P01031
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M magnesium formate dehydrate, 15.0% w/v polyethylene glycol 3350, 20% v/v glycerol as cryoprotectant

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.11→42.49 Å / Num. obs: 56154 / % possible obs: 92.1 % / Redundancy: 2 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 7.9
Reflection shellResolution: 2.11→2.16 Å / Redundancy: 2 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 1.8 / % possible all: 95.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata processing
Aimlessdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BBJ, 3CU7

1bbj

3cu7
PDB Unreleased entry


Resolution: 2.11→25 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.92 / SU B: 9.455 / SU ML: 0.233 / SU R Cruickshank DPI: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.343 / ESU R Free: 0.247
RfactorNum. reflection% reflectionSelection details
Rfree0.2853 2724 4.9 %RANDOM
Rwork0.2459 ---
obs0.2478 53398 92.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 80.33 Å2 / Biso mean: 38.604 Å2 / Biso min: 16.15 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20.86 Å21.39 Å2
2---0.39 Å21.52 Å2
3----0.79 Å2
Refinement stepCycle: final / Resolution: 2.11→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7895 0 0 322 8217
Biso mean---39.29 -
Num. residues----1057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198085
X-RAY DIFFRACTIONr_angle_refined_deg1.0621.94211004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.82751047
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22924.161298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38151228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5721524
X-RAY DIFFRACTIONr_chiral_restr0.060.21256
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216030
X-RAY DIFFRACTIONr_mcbond_it0.7173.9344218
X-RAY DIFFRACTIONr_mcangle_it1.3325.8925255
X-RAY DIFFRACTIONr_scbond_it0.463.8983867
LS refinement shellResolution: 2.11→2.164 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 210 -
Rwork0.357 4034 -
all-4244 -
obs--95.74 %

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