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- PDB-7tv9: HUMAN COMPLEMENT COMPONENT C3B IN COMPLEX WITH APL-1030 -

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Basic information

Entry
Database: PDB / ID: 7tv9
TitleHUMAN COMPLEMENT COMPONENT C3B IN COMPLEX WITH APL-1030
Components
  • APL-1030 Nanofitin
  • Complement C3 beta chain
  • Complement C3b alpha' chain
KeywordsIMMUNE SYSTEM / complement protein complex
Function / homology
Function and homology information


oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of lipid storage ...oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of lipid storage / positive regulation of phagocytosis, engulfment / complement receptor mediated signaling pathway / Activation of C3 and C5 / positive regulation of type IIa hypersensitivity / positive regulation of glucose transmembrane transport / complement-dependent cytotoxicity / complement activation, alternative pathway / complement activation / neuron remodeling / endopeptidase inhibitor activity / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / Peptide ligand-binding receptors / fatty acid metabolic process / complement activation, classical pathway / Regulation of Complement cascade / Post-translational protein phosphorylation / response to bacterium / positive regulation of receptor-mediated endocytosis / positive regulation of angiogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / G alpha (i) signalling events / secretory granule lumen / blood microparticle / inflammatory response / positive regulation of protein phosphorylation / immune response / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / : ...: / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / : / Alpha-macro-globulin thiol-ester bond-forming region / 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 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / 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 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsFontano, E. / Nadupalli, A. / Lakshminarasimhan, D. / White, A. / Garlish, J. / Cinier, M. / Chevrel, A. / Perrocheau, A. / Eyerman, D. / Orme, M. ...Fontano, E. / Nadupalli, A. / Lakshminarasimhan, D. / White, A. / Garlish, J. / Cinier, M. / Chevrel, A. / Perrocheau, A. / Eyerman, D. / Orme, M. / Kitten, O. / Scheibler, L.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Biomolecules / Year: 2022
Title: Discovery of APL-1030, a Novel, High-Affinity Nanofitin Inhibitor of C3-Mediated Complement Activation.
Authors: Garlich, J. / Cinier, M. / Chevrel, A. / Perrocheau, A. / Eyerman, D.J. / Orme, M. / Kitten, O. / Scheibler, L.
History
DepositionFeb 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement C3 beta chain
B: Complement C3b alpha' chain
C: APL-1030 Nanofitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,6565
Polymers182,8483
Non-polymers8082
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12900 Å2
ΔGint-59 kcal/mol
Surface area71560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.481, 104.699, 103.115
Angle α, β, γ (deg.)90.000, 97.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Complement C3 beta chain


Mass: 71393.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Plasmid details: SECRETION: SERUM / References: UniProt: P01024
#2: Protein Complement C3b alpha' chain


Mass: 104073.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Plasmid details: SECRETION: SERUM / References: UniProt: P01024
#3: Protein APL-1030 Nanofitin


Mass: 7381.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli DH5[alpha] (bacteria)
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}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.: 1 / 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
Has ligand of interestN

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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: 2.91 Å3/Da / Density % sol: 57.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 100 mM HEPES, pH 7.8, 25% Poly(acrylic acid sodium salt) 5100

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 3.4→98.83 Å / Num. obs: 28812 / % possible obs: 99.2 % / Redundancy: 3.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.102 / Rrim(I) all: 0.185 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.1 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.4-3.611.4921429245760.461.0031.8040.998.1
10.2-98.640.029340011110.9980.0190.03425.898.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2i07

2i07


Resolution: 3.4→98.83 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.866 / SU B: 146.1 / SU ML: 0.921 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.771 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3275 1347 4.7 %RANDOM
Rwork0.2395 ---
obs0.2436 27449 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 223.61 Å2 / Biso mean: 126.607 Å2 / Biso min: 88.84 Å2
Baniso -1Baniso -2Baniso -3
1--3.19 Å20 Å2-2.77 Å2
2---3.36 Å20 Å2
3---7.04 Å2
Refinement stepCycle: final / Resolution: 3.4→98.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12626 0 53 0 12679
Biso mean--166.42 --
Num. residues----1601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01312939
X-RAY DIFFRACTIONr_bond_other_d0.0020.01712376
X-RAY DIFFRACTIONr_angle_refined_deg1.0321.65217552
X-RAY DIFFRACTIONr_angle_other_deg0.9641.58528589
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.82151595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33323.38648
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.161152299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3311568
X-RAY DIFFRACTIONr_chiral_restr0.030.21708
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0214508
X-RAY DIFFRACTIONr_gen_planes_other0.0090.022817
LS refinement shellResolution: 3.4→3.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.474 93 -
Rwork0.428 1935 -
all-2028 -
obs--95.57 %
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)
11.30010.33060.64980.60350.2890.5440.037-0.08720.00130.068-0.01070.00670.0324-0.0099-0.02620.10880.00830.20640.7351-0.04050.426558.148-15.29-2.375
20.94790.50770.51590.7361-0.05250.5544-0.0083-0.0043-0.1872-0.11490.08710.00660.09290.0319-0.07880.0636-0.03220.12610.6374-0.05420.699627.295-37.763-22.192
33.15970.79382.41610.75921.68224.9337-0.0206-0.036-0.27860.232-0.08050.08010.32690.10550.10120.49740.04880.02940.31640.02150.492415.352-21.06717.571
42.15680.22680.45382.7204-0.1362.21460.0301-0.2459-0.16680.8490.12010.16760.037-0.1916-0.15030.40610.15580.17960.85980.02980.323456.638-7.80252.839
51.16990.82150.05730.63550.48513.60880.2759-0.395-0.24470.2893-0.263-0.16990.5191-0.16-0.01290.53840.04450.03740.53040.0920.705121.053-26.18119.611
62.03280.99510.12363.16410.13151.9498-0.18190.22970.2413-0.07640.24880.51630.07350.0888-0.06690.02790.01670.03470.67460.04330.649510.525-16.02-32.709
73.10150.88750.40794.34170.05632.0715-0.17270.41480.1845-0.141-0.13890.580.2093-0.10560.31170.0919-0.08570.14260.5745-0.05460.709-17.282-45.075-19.571
83.3818-2.4250.70841.8448-1.03542.89870.25550.10540.1943-0.0826-0.1552-0.1403-0.52930.403-0.10030.189-0.11640.20020.689-0.14210.59889.728-0.834-12.774
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 642
2X-RAY DIFFRACTION2B730 - 911
3X-RAY DIFFRACTION3B912 - 965
4X-RAY DIFFRACTION4B966 - 1269
5X-RAY DIFFRACTION5B1270 - 1331
6X-RAY DIFFRACTION6B1332 - 1480
7X-RAY DIFFRACTION7B1481 - 1641
8X-RAY DIFFRACTION8C1 - 63

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