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- PDB-8ivd: COMPLEX STRUCTURE OF CD93-IGFBP7 -

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Basic information

Entry
Database: PDB / ID: 8ivd
TitleCOMPLEX STRUCTURE OF CD93-IGFBP7
ComponentsInsulin-like growth factor-binding protein 7,Complement component C1q receptor
KeywordsCELL ADHESION / Complex structure / immune regulation / adhesion / tumor suppression
Function / homology
Function and homology information


regulation of steroid biosynthetic process / complement component C1q complex binding / insulin-like growth factor binding / response to cortisol / macrophage activation / tertiary granule membrane / ficolin-1-rich granule membrane / regulation of signal transduction / response to retinoic acid / phagocytosis ...regulation of steroid biosynthetic process / complement component C1q complex binding / insulin-like growth factor binding / response to cortisol / macrophage activation / tertiary granule membrane / ficolin-1-rich granule membrane / regulation of signal transduction / response to retinoic acid / phagocytosis / specific granule membrane / cellular response to hormone stimulus / embryo implantation / secretory granule membrane / Post-translational protein phosphorylation / regulation of cell growth / cell-cell adhesion / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / signaling receptor activity / : / carbohydrate binding / Senescence-Associated Secretory Phenotype (SASP) / angiogenesis / cell adhesion / endoplasmic reticulum lumen / negative regulation of cell population proliferation / calcium ion binding / Neutrophil degranulation / cell surface / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Insulin-like growth factor binding protein-related protein (IGFBP-rP), MAC25 / Insulin-like growth factor binding protein / Insulin-like growth factor-binding protein, IGFBP / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain profile. / Insulin growth factor-binding protein homologues / Complement Clr-like EGF domain / Complement Clr-like EGF-like / Kazal-type serine protease inhibitor domain / Kazal type serine protease inhibitors ...: / Insulin-like growth factor binding protein-related protein (IGFBP-rP), MAC25 / Insulin-like growth factor binding protein / Insulin-like growth factor-binding protein, IGFBP / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain profile. / Insulin growth factor-binding protein homologues / Complement Clr-like EGF domain / Complement Clr-like EGF-like / Kazal-type serine protease inhibitor domain / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / : / Calcium-binding EGF domain / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / 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 / Immunoglobulin I-set / Immunoglobulin I-set domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Insulin-like growth factor-binding protein 7 / Complement component C1q receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.24 Å
AuthorsXu, Y.M. / Song, G.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171215 China
CitationJournal: Structure / Year: 2024
Title: Structural insight into CD93 recognition by IGFBP7.
Authors: Xu, Y. / Sun, Y. / Zhu, Y. / Song, G.
History
DepositionMar 27, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Oct 30, 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: Insulin-like growth factor-binding protein 7,Complement component C1q receptor
B: Insulin-like growth factor-binding protein 7,Complement component C1q receptor
C: Insulin-like growth factor-binding protein 7,Complement component C1q receptor
D: Insulin-like growth factor-binding protein 7,Complement component C1q receptor


Theoretical massNumber of molelcules
Total (without water)201,3174
Polymers201,3174
Non-polymers00
Water30617
1
A: Insulin-like growth factor-binding protein 7,Complement component C1q receptor
D: Insulin-like growth factor-binding protein 7,Complement component C1q receptor


Theoretical massNumber of molelcules
Total (without water)100,6592
Polymers100,6592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-7 kcal/mol
Surface area19200 Å2
MethodPISA
2
B: Insulin-like growth factor-binding protein 7,Complement component C1q receptor
C: Insulin-like growth factor-binding protein 7,Complement component C1q receptor


Theoretical massNumber of molelcules
Total (without water)100,6592
Polymers100,6592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-7 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.512, 208.895, 77.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein
Insulin-like growth factor-binding protein 7,Complement component C1q receptor / IBP-7 / IGF-binding protein 7 / IGFBP-7 / IGFBP-rP1 / MAC25 protein / PGI2-stimulating factor / ...IBP-7 / IGF-binding protein 7 / IGFBP-7 / IGFBP-rP1 / MAC25 protein / PGI2-stimulating factor / Prostacyclin-stimulating factor / Tumor-derived adhesion factor / TAF / C1q/MBL/SPA receptor / C1qR / C1qR(p) / C1qRp / CDw93 / Complement component 1 q subcomponent receptor 1 / Matrix-remodeling-associated protein 4


Mass: 50329.371 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The depositor stated, 'for the large gap, we agree that the distance between C-ter of chainC and N-ter of Chain B is too large (~60 A) that the linker can not cover the gap, that's why we ...Details: The depositor stated, 'for the large gap, we agree that the distance between C-ter of chainC and N-ter of Chain B is too large (~60 A) that the linker can not cover the gap, that's why we doubt that these two are in a single chain and Chain C is possible to linker to chainA as their distance is ~12A. As this is not conclusive since the densities for linker are missing i suggest we name these chains (A-D) individually as i submitted, and this numbering method has been used by many other researcher, and will benefit the reader (as the numbering will be consistent with their nature numbering).'
Source: (gene. exp.) Homo sapiens (human) / Gene: IGFBP7, MAC25, PSF, CD93, C1QR1, MXRA4 / Production host: Homo sapiens (human) / References: UniProt: Q16270, UniProt: Q9NPY3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.31 Å3/Da / Density % sol: 62.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M imidazole, 20% w/v PEG monomethyl ether 2000, and 0.2 M ammonium citrate tribasic pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: LN / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 1, 2022
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.24→48.2 Å / Num. obs: 17340 / % possible obs: 99.9 % / Redundancy: 12 % / Biso Wilson estimate: 118.44 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.09 / Rrim(I) all: 0.2 / Rsym value: 0.2 / Χ2: 0.99 / Net I/σ(I): 9.4
Reflection shellResolution: 3.24→3.5 Å / Redundancy: 10.4 % / Rmerge(I) obs: 2.14 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3495 / CC1/2: 0.48 / Rpim(I) all: 1 / Χ2: 1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Coot1.20.1_4487model building
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.24→19.95 Å / SU ML: 0.5592 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.1671
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3018 849 4.92 %
Rwork0.2437 16399 -
obs0.2464 17248 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 143.97 Å2
Refinement stepCycle: LAST / Resolution: 3.24→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5364 0 0 17 5381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00195483
X-RAY DIFFRACTIONf_angle_d0.4647452
X-RAY DIFFRACTIONf_chiral_restr0.0371811
X-RAY DIFFRACTIONf_plane_restr0.00551003
X-RAY DIFFRACTIONf_dihedral_angle_d3.4984793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.24-3.440.39091480.37432650X-RAY DIFFRACTION99.61
3.44-3.710.38881260.32392726X-RAY DIFFRACTION99.89
3.71-4.080.33051520.26812683X-RAY DIFFRACTION99.86
4.08-4.660.27551300.2312731X-RAY DIFFRACTION99.97
4.66-5.850.29261550.23182754X-RAY DIFFRACTION99.97
5.85-19.950.2731380.21422855X-RAY DIFFRACTION99.67
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)
11.91735336202-0.282373486299-0.1807152714474.85159987796-0.2052201343241.625161950080.05455164900420.292918856152-0.209260905444-0.789888667965-0.0495366142443-1.01465431090.3560778332380.2803193652450.02181274913171.01271888619-0.0449913871580.1549028314650.912012090283-0.1336520159281.2312956362-36.2112503889-3.61498716573-10.9788369256
27.20611493047-0.465994362155-4.352041389841.062712111760.9592765258442.318420574040.4485829099760.2520983776850.025374409469-0.292931005308-0.127874347129-0.0968784796915-0.2625763938020.0354100085607-0.3316173759341.093150961720.203239850907-0.1132724236371.19770536238-0.04694938438441.0836102467-24.6070480353-41.1891833777-30.1181637208
34.23511847008-0.3576497266921.001368923463.82313310728-0.6491822100867.371258827760.08244464788650.1629163933460.2689200079770.03609640885540.280727670198-0.216011254137-0.3977387870980.201014308924-0.3932926921930.6973406535440.04545379434190.02173888949240.9170615043570.004279928596580.760366336957-56.8954622084-28.3938416659-11.2411905446
42.677482309710.7078400005410.2011216726384.740326113531.957648430575.44713630560.151247936130.04351007235950.803073751201-0.6517405552710.03547068710920.0483006079904-0.3562380735570.778911802537-0.2700206716071.500480555180.01456584152270.4868325156621.188178715920.1016237946331.6854412636-34.989802081937.2746981717-15.3090787558
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A'AA26 - 3041 - 274
22chain 'B'BB26 - 3041 - 267
33chain 'C'CC31 - 1581 - 115
44chain 'D'DE31 - 1571 - 108

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