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- PDB-7do4: Crystal structure of CD97-CD55 complex -

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Basic information

Entry
Database: PDB / ID: 7do4
TitleCrystal structure of CD97-CD55 complex
Components
  • Complement decay-accelerating factor
  • Isoform 2 of Adhesion G protein-coupled receptor E5
KeywordsIMMUNE SYSTEM / ligand-receptor / signalling / IMMUNE disorder
Function / homology
Function and homology information


regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / negative regulation of complement activation, classical pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / T cell mediated immunity / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) ...regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / negative regulation of complement activation, classical pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / T cell mediated immunity / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / ficolin-1-rich granule membrane / side of membrane / COPI-mediated anterograde transport / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / secretory granule membrane / complement activation, classical pathway / Regulation of Complement cascade / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of T cell cytokine production / transmembrane signaling receptor activity / cell-cell signaling / virus receptor activity / positive regulation of cytosolic calcium ion concentration / cell surface receptor signaling pathway / cell adhesion / inflammatory response / immune response / G protein-coupled receptor signaling pathway / membrane raft / Golgi membrane / innate immune response / focal adhesion / lipid binding / calcium ion binding / Neutrophil degranulation / cell surface / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
GPCR, family 2, ADGRE2/ADGRE5 / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / : / Calcium-binding EGF domain / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) ...GPCR, family 2, ADGRE2/ADGRE5 / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / : / Calcium-binding EGF domain / 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 / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain
Similarity search - Domain/homology
Complement decay-accelerating factor / Adhesion G protein-coupled receptor E5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsNiu, M. / Song, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770898 China
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural basis for CD97 recognition of the decay-accelerating factor CD55 suggests mechanosensitive activation of adhesion GPCRs.
Authors: Niu, M. / Xu, S. / Yang, J. / Yao, D. / Li, N. / Yan, J. / Zhong, G. / Song, G.
History
DepositionDec 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Assembly

Deposited unit
A: Isoform 2 of Adhesion G protein-coupled receptor E5
B: Complement decay-accelerating factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5787
Polymers43,6312
Non-polymers9475
Water34219
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, the 1:1 binding model fits well with the SAXS envelop of the protein complex in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.800, 44.250, 116.530
Angle α, β, γ (deg.)90.000, 98.700, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Isoform 2 of Adhesion G protein-coupled receptor E5 / Leukocyte antigen CD97


Mass: 15789.192 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADGRE5, CD97 / Organ: KIDENY / Variant: EGF1 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: P48960
#2: Protein Complement decay-accelerating factor


Mass: 27842.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD55, CR, DAF / Variant: 2 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: P08174

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Sugars , 2 types, 3 molecules

#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

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Non-polymers , 2 types, 21 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Sequence detailsTHIS SEQUENCE CORRESPONDS TO THE ISOFORM-2 FOUND IN UNP P08174.

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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: 2.8 Å3/Da / Density % sol: 59.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 5.9 and 10% PEG20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 1, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3.19→33.23 Å / Num. obs: 8903 / % possible obs: 99.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 80.35 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.14 / Χ2: 0.88 / Net I/σ(I): 7.3
Reflection shellResolution: 3.19→3.27 Å / Redundancy: 4 % / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 641 / CC1/2: 0.895 / Χ2: 0.89 / % possible all: 98.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BOU, 1OJV

2bou

1ojv


Resolution: 3.2→33.226 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 37.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3044 882 10.05 %
Rwork0.267 7896 -
obs0.2708 8778 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 193.38 Å2 / Biso mean: 80.35 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.2→33.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2947 0 58 19 3024
Biso mean--130.37 54.81 -
Num. residues----391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043100
X-RAY DIFFRACTIONf_angle_d0.8994242
X-RAY DIFFRACTIONf_chiral_restr0.057458
X-RAY DIFFRACTIONf_plane_restr0.006561
X-RAY DIFFRACTIONf_dihedral_angle_d15.8711888
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2002-3.40050.41461460.382128998
3.4005-3.66270.36271400.3458130399
3.6627-4.03080.34281460.2943131699
4.0308-4.61270.26221440.2616130299
4.6127-5.80650.28131500.24711330100
5.8065-33.220.28531560.2212135698
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)
11.59010.33530.59631.22490.512.48930.0933-0.2121-0.30740.06480.0917-0.08130.0281-0.3039-0.16551.07480.0513-0.16790.6314-0.0070.7698-9.2128-24.277236.6598
20.39450.29250.47730.80650.57361.9284-0.02570.0156-0.09050.00160.1548-0.0879-0.28690.5455-0.22930.5848-0.00880.00990.6206-0.04140.60885.0848-2.72262.4133
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 164 )A25 - 164
2X-RAY DIFFRACTION2chain 'B' and (resid 34 through 284 )B34 - 284

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