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- PDB-8voh: HADDOCK models of human alphaM I-domain bound to the the N-termin... -

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Basic information

Entry
Database: PDB / ID: 8voh
TitleHADDOCK models of human alphaM I-domain bound to the the N-terminal domain of the cytokine pleiotrophin
Components
  • Integrin alpha-M
  • Pleiotrophin
KeywordsCELL ADHESION / integrin / Mac-1 / pleiotrophin
Function / homology
Function and homology information


dendrite regeneration / ossification involved in bone remodeling / ectodermal cell differentiation / cell surface receptor protein tyrosine phosphatase signaling pathway / response to curcumin / chondroitin sulfate binding / positive regulation of neutrophil degranulation / integrin alphaM-beta2 complex / leukocyte chemotaxis involved in inflammatory response / response to Gram-positive bacterium ...dendrite regeneration / ossification involved in bone remodeling / ectodermal cell differentiation / cell surface receptor protein tyrosine phosphatase signaling pathway / response to curcumin / chondroitin sulfate binding / positive regulation of neutrophil degranulation / integrin alphaM-beta2 complex / leukocyte chemotaxis involved in inflammatory response / response to Gram-positive bacterium / regulation of stem cell population maintenance / regulation of endothelial cell migration / positive regulation of microglial cell mediated cytotoxicity / MDK and PTN in ALK signaling / dendrite arborization / tissue regeneration / cell-cell adhesion via plasma-membrane adhesion molecules / complement component C3b binding / vertebrate eye-specific patterning / response to auditory stimulus / complement-mediated synapse pruning / negative regulation of dopamine metabolic process / positive regulation of stem cell differentiation / Toll Like Receptor 4 (TLR4) Cascade / positive regulation of leukocyte chemotaxis / complement receptor mediated signaling pathway / positive regulation of ossification / positive regulation of hepatocyte proliferation / integrin complex / heterotypic cell-cell adhesion / cargo receptor activity / positive regulation of dendrite development / regulation of myelination / regulation of hemopoiesis / negative regulation of neuroblast proliferation / Signaling by ALK / phagocytosis, engulfment / cell adhesion mediated by integrin / oogenesis / protein phosphatase inhibitor activity / receptor clustering / positive regulation of axon regeneration / bone mineralization / amyloid-beta clearance / tertiary granule membrane / positive regulation of cell division / positive regulation of oligodendrocyte differentiation / decidualization / negative regulation of long-term synaptic potentiation / plasma membrane raft / positive regulation of protein targeting to membrane / Integrin cell surface interactions / positive regulation of bone mineralization / specific granule membrane / response to mechanical stimulus / forebrain development / estrous cycle / heat shock protein binding / receptor-mediated endocytosis / molecular function activator activity / positive regulation of superoxide anion generation / learning / cell-matrix adhesion / response to ischemia / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / growth factor activity / microglial cell activation / Schaffer collateral - CA1 synapse / cell-cell adhesion / regulation of synaptic plasticity / positive regulation of neuron projection development / memory / integrin binding / nervous system development / response to estradiol / heparin binding / amyloid-beta binding / carbohydrate binding / Interleukin-4 and Interleukin-13 signaling / cell adhesion / external side of plasma membrane / innate immune response / positive regulation of cell population proliferation / Neutrophil degranulation / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Pleiotrophin/Midkine heparin-binding growth factor, conserved site / PTN/MK heparin-binding protein family signature 1. / PTN/MK heparin-binding protein family signature 2. / Midkine heparin-binding growth factor / Pleiotrophin/Midkine, N-terminal domain / Pleiotrophin/Midkine, C-terminal domain / Pleiotrophin/Midkine disulphide-rich domain superfamily / Pleiotrophin/Midkine, N-terminal domain superfamily / Pleiotrophin/Midkine, C-terminal domain superfamily / PTN/MK heparin-binding protein family, C-terminal domain ...Pleiotrophin/Midkine heparin-binding growth factor, conserved site / PTN/MK heparin-binding protein family signature 1. / PTN/MK heparin-binding protein family signature 2. / Midkine heparin-binding growth factor / Pleiotrophin/Midkine, N-terminal domain / Pleiotrophin/Midkine, C-terminal domain / Pleiotrophin/Midkine disulphide-rich domain superfamily / Pleiotrophin/Midkine, N-terminal domain superfamily / Pleiotrophin/Midkine, C-terminal domain superfamily / PTN/MK heparin-binding protein family, C-terminal domain / PTN/MK heparin-binding protein family, N-terminal domain / Pleiotrophin / midkine family / : / Integrin alpha-X-like, Ig-like domain 3 / Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
Integrin alpha-M / Pleiotrophin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWang, X. / Nguyen, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118518 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL063199 United States
CitationJournal: Structure / Year: 2024
Title: alpha M I-domain of integrin Mac-1 binds the cytokine pleiotrophin using multiple mechanisms.
Authors: Nguyen, H. / Podolnikova, N.P. / Ugarova, T.P. / Wang, X.
History
DepositionJan 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.2May 28, 2025Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin alpha-M
B: Pleiotrophin


Theoretical massNumber of molelcules
Total (without water)28,6702
Polymers28,6702
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1370 Å2
ΔGint-0 kcal/mol
Surface area14160 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200target function
RepresentativeModel #1target function

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Components

#1: Protein Integrin alpha-M / CD11 antigen-like family member B / CR-3 alpha chain / Cell surface glycoprotein MAC-1 subunit ...CD11 antigen-like family member B / CR-3 alpha chain / Cell surface glycoprotein MAC-1 subunit alpha / Leukocyte adhesion receptor MO1 / Neutrophil adherence receptor


Mass: 22238.340 Da / Num. of mol.: 1 / Fragment: I-domain, residues 147-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAM, CD11B, CR3A / Production host: Escherichia coli (E. coli) / References: UniProt: P11215
#2: Protein Pleiotrophin / PTN / Heparin-binding brain mitogen / HBBM / Heparin-binding growth factor 8 / HBGF-8 / Heparin- ...PTN / Heparin-binding brain mitogen / HBBM / Heparin-binding growth factor 8 / HBGF-8 / Heparin-binding growth-associated molecule / HB-GAM / Heparin-binding neurite outgrowth-promoting factor / HBNF / Heparin-binding neurite outgrowth-promoting factor 1 / HBNF-1 / Osteoblast-specific factor 1 / OSF-1


Mass: 6431.449 Da / Num. of mol.: 1 / Fragment: N-terminal domain, residues 33-90
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTN, HBNF1, NEGF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P21246
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D F1-13C-edited/F3-13C,15N-filtered HSQCNOESY
122isotropic13D (H)CCH-TOCSY
133isotropic13D (H)CCH-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.2 mM [U-13C; U-15N] human alphaM I-domain, 1 mM The N-terminal domain of pleiotrophin, 90% H2O/10% D2O13C,15N-alphaM I-domain, unlabeled PTN-NTD90% H2O/10% D2O
solution20.5 mM [U-13C; U-15N] human alphaM I-domain, 90% H2O/10% D2O13C,15N-alphaM I-domain90% H2O/10% D2O
solution30.5 mM [U-13C; U-15N] The N-terminal domain of pleiotrophin, 90% H2O/10% D2O13C,15N-PTN-NTD90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMhuman alphaM I-domain[U-13C; U-15N]1
1 mMThe N-terminal domain of pleiotrophinnatural abundance1
0.5 mMhuman alphaM I-domain[U-13C; U-15N]2
0.5 mMThe N-terminal domain of pleiotrophin[U-13C; U-15N]3
Sample conditionsIonic strength: 0.1 M / Ionic strength err: 0.01 / Label: HEPES / pH: 7 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.1

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 850 MHz

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Processing

NMR software
NameDeveloperClassification
NMRViewJBruce Johnsonchemical shift assignment
HADDOCKBonvinstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 2
Details: The Integrin alpha-M starting structure is 1JLM. The Pleiotrophin starting structure is 2N6F.
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 10

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