[English] 日本語
Yorodumi
- PDB-8eo2: Lufaxin a bifunctional inhibitor of complement and coagulation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8eo2
TitleLufaxin a bifunctional inhibitor of complement and coagulation
ComponentsLufaxin
KeywordsBLOOD CLOTTING / complement / coagulation / sand fly / salivary / inhibitor
Function / homologytoxin activity / extracellular region / BROMIDE ION / Lufaxin
Function and homology information
Biological speciesLutzomyia longipalpis (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.31 Å
AuthorsAndersen, J.F. / Strayer, E.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Blood / Year: 2023
Title: A bispecific inhibitor of complement and coagulation blocks activation in complementopathy models via a novel mechanism.
Authors: John F Andersen / Haotian Lei / Ethan C Strayer / Tapan Kanai / Van Pham / Xiang-Zuo Pan / Patricia Hessab Alvarenga / Gloria F Gerber / Oluwatoyin A Asojo / Ivo M B Francischetti / Robert A ...Authors: John F Andersen / Haotian Lei / Ethan C Strayer / Tapan Kanai / Van Pham / Xiang-Zuo Pan / Patricia Hessab Alvarenga / Gloria F Gerber / Oluwatoyin A Asojo / Ivo M B Francischetti / Robert A Brodsky / Jesus G Valenzuela / José M C Ribeiro /
Abstract: Inhibitors of complement and coagulation are present in the saliva of a variety of blood-feeding arthropods that transmit parasitic and viral pathogens. Here, we describe the structure and mechanism ...Inhibitors of complement and coagulation are present in the saliva of a variety of blood-feeding arthropods that transmit parasitic and viral pathogens. Here, we describe the structure and mechanism of action of the sand fly salivary protein lufaxin, which inhibits the formation of the central alternative C3 convertase (C3bBb) and inhibits coagulation factor Xa (fXa). Surface plasmon resonance experiments show that lufaxin stabilizes the binding of serine protease factor B (FB) to C3b but does not detectably bind either C3b or FB alone. The crystal structure of the inhibitor reveals a novel all β-sheet fold containing 2 domains. A structure of the lufaxin-C3bB complex obtained via cryo-electron microscopy (EM) shows that lufaxin binds via its N-terminal domain at an interface containing elements of both C3b and FB. By occupying this spot, the inhibitor locks FB into a closed conformation in which proteolytic activation of FB by FD cannot occur. C3bB-bound lufaxin binds fXa at a separate site in its C-terminal domain. In the cryo-EM structure of a C3bB-lufaxin-fXa complex, the inhibitor binds to both targets simultaneously, and lufaxin inhibits fXa through substrate-like binding of a C-terminal peptide at the active site as well as other interactions in this region. Lufaxin inhibits complement activation in ex vivo models of atypical hemolytic uremic syndrome (aHUS) and paroxysmal nocturnal hemoglobinuria (PNH) as well as thrombin generation in plasma, providing a rationale for the development of a bispecific inhibitor to treat complement-related diseases in which thrombosis is a prominent manifestation.
History
DepositionOct 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lufaxin
B: Lufaxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,65412
Polymers66,7092
Non-polymers1,94510
Water2,576143
1
A: Lufaxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4947
Polymers33,3551
Non-polymers1,1406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lufaxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1605
Polymers33,3551
Non-polymers8054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.480, 71.310, 167.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Lufaxin / 32.4 kDa salivary protein / Lutzomyia longipalpis FXa inhibitor


Mass: 33354.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lutzomyia longipalpis (insect) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q5WPU8

-
Sugars , 3 types, 4 molecules

#2: 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
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}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.: 2 / 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

-
Non-polymers , 3 types, 149 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Br
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.34 % / Description: rectangular plates
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 10% PEG 6000, 100 mM Tris HCl, pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.31→42.18 Å / Num. obs: 34638 / % possible obs: 99.9 % / Redundancy: 8.745 % / Biso Wilson estimate: 49.71 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.06 / Χ2: 1.07 / Net I/σ(I): 21.15 / Num. measured all: 302907 / Scaling rejects: 101
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.31-2.378.0040.5534.1220203252725240.9390.59299.9
2.37-2.438.8460.4615.1521576244024390.9610.49100
2.43-2.519.4860.3836.3422815240624050.9690.406100
2.51-2.589.430.2987.9221990233323320.9820.315100
2.58-2.679.3890.2359.8321087224622460.9870.249100
2.67-2.769.2370.18611.8820321220022000.9910.197100
2.76-2.879.1960.14414.4219266209520950.9950.153100
2.87-2.989.0520.11517.518521204620460.9970.122100
2.98-3.118.9170.08921.0717486196119610.9980.095100
3.11-3.278.4930.07525.1415975188318810.9980.0899.9
3.27-3.447.5240.0628.1113393178317800.9980.06499.8
3.44-3.658.7610.05234.7214744168516830.9990.05599.9
3.65-3.98.9690.04837.5714413160716070.9990.051100
3.9-4.228.7940.04439.5313208150215020.9990.047100
4.22-4.628.6320.04141.6111930138213820.9990.044100
4.62-5.178.3560.03942.1510428125012480.9990.04299.8
5.17-5.968.0570.03940.749121113511320.9990.04199.7
5.96-7.37.0760.03938.5467799599580.9990.04299.9
7.3-10.338.3740.03543.6963817627620.9990.037100
10.33-42.187.1870.03440.8532704614550.9990.03698.7

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19.2refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.31→42.18 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.52 / Phase error: 27.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 1638 4.86 %
Rwork0.2012 32091 -
obs0.2039 33729 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.15 Å2 / Biso mean: 59.9233 Å2 / Biso min: 29.87 Å2
Refinement stepCycle: final / Resolution: 2.31→42.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4437 0 114 143 4694
Biso mean--66.34 52.39 -
Num. residues----545
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.31-2.380.3161130.24372499261292
2.38-2.450.33391360.23012513264993
2.45-2.540.31791370.22712541267894
2.54-2.640.29171170.23252605272296
2.64-2.760.29231270.25752652277998
2.76-2.910.3511530.25592644279798
2.91-3.090.30221560.23042700285699
3.09-3.330.28481370.21842703284099
3.33-3.670.23251250.198527502875100
3.67-4.20.24841560.172327522908100
4.2-5.280.18971300.159428012931100
5.29-42.180.241510.208329313082100
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)
16.3239-0.05291.27118.60382.43556.9191-0.2029-0.41920.00680.32050.4579-0.09040.2185-0.365-0.23880.4110.0281-0.07120.4780.0520.2125-16.9795-5.1888-17.524
20.4184-0.8323-0.80987.04561.12516.4804-0.0438-0.02290.17670.01180.20750.22270.041-0.6563-0.15670.29660.0159-0.09530.4062-0.02080.2815-19.8699-2.0156-24.2648
31.84051.28372.58362.79992.26125.87610.20460.1051-0.3204-0.11490.05640.30930.7046-0.4293-0.26860.5259-0.0501-0.13910.46550.0380.445-25.104-17.6493-38.2255
43.11791.04130.32635.09451.25083.8427-0.00990.6253-0.4388-0.27940.3849-0.29290.5610.5406-0.35920.48850.032-0.14610.5278-0.08570.4327-16.6545-17.9194-47.6056
55.0235-0.52470.99183.8918-1.24047.5330.39840.592-0.1066-0.8012-0.22470.12610.0188-0.2318-0.16850.55250.14510.04060.5319-0.10870.292-36.4424-37.0965-16.8284
63.1595-0.09861.04312.66940.04084.51190.05440.16390.256-0.1942-0.1069-0.4651-0.48960.6550.03750.4014-0.05220.10130.38970.06010.4308-26.2788-24.2151-0.6006
74.74850.71261.5445.01780.28325.83590.1715-0.30330.00030.5296-0.1996-0.519-0.11870.37540.01560.3352-0.05150.04370.35-0.00040.3366-25.4679-31.029110.1711
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 36 )A1 - 36
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 100 )A37 - 100
3X-RAY DIFFRACTION3chain 'A' and (resid 101 through 179 )A101 - 179
4X-RAY DIFFRACTION4chain 'A' and (resid 180 through 274 )A180 - 274
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 100 )B1 - 100
6X-RAY DIFFRACTION6chain 'B' and (resid 101 through 179 )B101 - 179
7X-RAY DIFFRACTION7chain 'B' and (resid 180 through 272 )B180 - 272

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more