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- PDB-6o6w: Solution structure of human myeloid-derived growth factor -

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Basic information

Entry
Database: PDB / ID: 6o6w
TitleSolution structure of human myeloid-derived growth factor
ComponentsMyeloid-derived growth factor
KeywordsUNKNOWN FUNCTION / Endoplasmic Reticulum / UPF0556
Function / homology
Function and homology information


XBP1(S) activates chaperone genes / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of endothelial cell proliferation / positive regulation of angiogenesis / angiogenesis / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / endoplasmic reticulum lumen / apoptotic process ...XBP1(S) activates chaperone genes / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of endothelial cell proliferation / positive regulation of angiogenesis / angiogenesis / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / endoplasmic reticulum lumen / apoptotic process / negative regulation of apoptotic process / Golgi apparatus / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / extracellular space
Similarity search - Function
Myeloid-derived growth factor / UPF0556 domain
Similarity search - Domain/homology
Myeloid-derived growth factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsBortnov, V. / Tonelli, M. / Lee, W. / Markley, J.L. / Mosher, D.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI125390-03 United States
CitationJournal: Nat Commun / Year: 2019
Title: Solution structure of human myeloid-derived growth factor suggests a conserved function in the endoplasmic reticulum.
Authors: Bortnov, V. / Tonelli, M. / Lee, W. / Lin, Z. / Annis, D.S. / Demerdash, O.N. / Bateman, A. / Mitchell, J.C. / Ge, Y. / Markley, J.L. / Mosher, D.F.
History
DepositionMar 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 2.0Jul 15, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Source and taxonomy
Category: atom_site / entity_src_gen ...atom_site / entity_src_gen / pdbx_nmr_ensemble / pdbx_struct_sheet_hbond / pdbx_validate_torsion / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant / _pdbx_nmr_ensemble.conformer_selection_criteria / _struct_conn.pdbx_dist_value / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id
Revision 2.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myeloid-derived growth factor


Theoretical massNumber of molelcules
Total (without water)16,2861
Polymers16,2861
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein Myeloid-derived growth factor / MYDGF


Mass: 16286.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Gene amplified from purified eosinophil RNA by RT-PCR.
Source: (gene. exp.) Homo sapiens (human) / Cell: human blood eosinophils / Gene: MYDGF, C19orf10 / Plasmid: pET-ELMER
Details (production host): pET28c(+) derivative (kanamycin resistance). Expresses proteins with N-terminal polyhistidine-tag followed by a thrombin cleavage site.
Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / Variant (production host): MilliporeSigma 71400 / References: UniProt: Q969H8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H,15N-HSQC NOESY
121isotropic13D 1H,13C-HSQC NOESY aliphatic
131isotropic13D 1H,13C-HSQC NOESY aromatic
141isotropic22D 1H-15N HSQC
151isotropic22D 1H-13C HSQC aliphatic
161isotropic12D 1H-13C HSQC aromatic
171isotropic23D CBCA(CO)NH
181isotropic23D HN(CA)CB
191isotropic23D HNCO
1101isotropic23D C(CO)NH
1111isotropic23D HBHA(CO)NH
1121isotropic23D (H)CCH-TOCSY aliphatic
1131isotropic23D H(CCO)NH
1141isotropic12D (HB)CB(CGCD)HD aromatic
1151isotropic12D (HB)CB(CGCDCE)HDHE aromatic
1161isotropic43D (H)CCH-TOCSY aromatic
1201isotropic33D 1H,15N-HSQC NOESY 1H,13C-HSQC

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Sample preparation

DetailsType: solution
Contents: 8.25 mg/mL U-15N; U-13C; NA-H MYDGF, 9 mM NA sodium phosphate, 135 mM NA sodium chloride, 15 uM NA DSS, 0.02 % w/v NA sodium azide, 90% H2O/10% D2O
Details: DSS was used as an internal NMR standard and sodium azide was added to prevent contamination growth.
Label: 15N_13C_MYDGF / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
8.25 mg/mLMYDGFU-15N; U-13C; NA-H1
9 mMsodium phosphateNA1
135 mMsodium chlorideNA1
15 uMDSSNA1
0.02 % w/vsodium azideNA1
Sample conditionsIonic strength: 135 (NaCl) mM / Label: Condition_1 / pH: 6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VNSVarianVNS8001
Bruker AVANCE IIIBrukerAVANCE III6002
Bruker AVANCE IIIBrukerAVANCE III9003
Varian VNSVarianVNS6004

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Processing

NMR software
NameVersionDeveloperClassification
VNMR4.2Variancollection
TopSpin3.5Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRFAM-SPARKYW. Lee, M. Tonelli and J.L. Markleychemical shift assignment
I-PINEW. Lee, A. Bahrami, H. Dashti, H.R. Eghbalnia, M. Tonelli, W.M. Westler, J.L. Markleychemical shift assignment
NMRFAM-SPARKYW. Lee, M. Tonelli and J.L. Markleypeak picking
PONDEROSA-C/SW. Lee, J.L. Stark, J.L. Markleystructure calculation
TALOS-NShen and Baxstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
PyMOLSchroedinger, Inc.refinement
PONDEROSA-C/SW. Lee, J.L. Stark, J.L. Markleyrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
Refinement
MethodSoftware ordinalDetails
molecular dynamics11explicit water refinement
molecular dynamics12explicit water refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 100 / Conformers submitted total number: 20

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