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- PDB-1emo: NMR STUDY OF A PAIR OF FIBRILLIN CA2+ BINDING EPIDERMAL GROWTH FA... -

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Basic information

Entry
Database: PDB / ID: 1emo
TitleNMR STUDY OF A PAIR OF FIBRILLIN CA2+ BINDING EPIDERMAL GROWTH FACTOR-LIKE DOMAINS, 22 STRUCTURES
ComponentsFIBRILLIN
KeywordsMATRIX PROTEIN / EXTRACELLULAR MATRIX / CALCIUM-BINDING / GLYCOPROTEIN / MULTIGENE FAMILY / DISEASE MUTATION / EGF-LIKE DOMAIN / HUMAN FIBRILLIN-1 FRAGMENT
Function / homology
Function and homology information


post-embryonic eye morphogenesis / extracellular matrix constituent conferring elasticity / sequestering of BMP in extracellular matrix / sequestering of TGFbeta in extracellular matrix / microfibril / embryonic eye morphogenesis / negative regulation of osteoclast development / metanephros development / camera-type eye development / Elastic fibre formation ...post-embryonic eye morphogenesis / extracellular matrix constituent conferring elasticity / sequestering of BMP in extracellular matrix / sequestering of TGFbeta in extracellular matrix / microfibril / embryonic eye morphogenesis / negative regulation of osteoclast development / metanephros development / camera-type eye development / Elastic fibre formation / extracellular matrix structural constituent / Molecules associated with elastic fibres / cell adhesion mediated by integrin / cellular response to insulin-like growth factor stimulus / lung alveolus development / negative regulation of osteoclast differentiation / TGF-beta receptor signaling activates SMADs / basement membrane / anatomical structure morphogenesis / Integrin cell surface interactions / cellular response to transforming growth factor beta stimulus / Degradation of the extracellular matrix / extracellular matrix / skeletal system development / Post-translational protein phosphorylation / hormone activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / integrin binding / heparin binding / heart development / gene expression / collagen-containing extracellular matrix / endoplasmic reticulum lumen / calcium ion binding / protein-containing complex binding / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Fibrillin 1, unique N-terminal domain / : / : / Fibrillin 1 unique N-terminal domain / Fibrillin, first EGF domain / TB domain / TB domain / TGF-beta binding (TB) domain superfamily / TGF-beta binding (TB) domain profile. / EGF domain ...Fibrillin 1, unique N-terminal domain / : / : / Fibrillin 1 unique N-terminal domain / Fibrillin, first EGF domain / TB domain / TB domain / TGF-beta binding (TB) domain superfamily / TGF-beta binding (TB) domain profile. / EGF domain / EGF domain / Complement Clr-like EGF domain / Complement Clr-like EGF-like / EGF-like, conserved site / Human growth factor-like EGF / : / Calcium-binding EGF domain / Laminin / Laminin / Coagulation Factor Xa inhibitory site / 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 signature 1. / EGF-like domain signature 2. / EGF-like domain / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsDowning, A.K. / Campbell, I.D. / Handford, P.A.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: Solution structure of a pair of calcium-binding epidermal growth factor-like domains: implications for the Marfan syndrome and other genetic disorders.
Authors: Downing, A.K. / Knott, V. / Werner, J.M. / Cardy, C.M. / Campbell, I.D. / Handford, P.A.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: Calcium Binding Properties of an Epidermal Growth Factor-Like Domain Pair from Human Fibrillin-1
Authors: Knott, V. / Downing, A.K. / Cardy, C.M. / Handford, P.
History
DepositionAug 5, 1996Processing site: BNL
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_related ...database_2 / pdbx_database_related / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.content_type / _pdbx_database_status.process_site / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_software.version / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FIBRILLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8313
Polymers8,7511
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)22 / 200F(NOE) < 165 KJ MOL-1 TORSION ANGLE CONSTRAINTS VIOLATED BY > 3 DEGREES
Representative

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Components

#1: Protein FIBRILLIN


Mass: 8750.710 Da / Num. of mol.: 1
Fragment: CA2+ BINDING EPIDERMAL GROWTH FACTOR-LIKE DOMAIN, RESIDUES 2124 - 2205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: SKIN (DERMIS) / Cell: FIBROBLAST / Gene: FBN1 / Organ: SKIN / Plasmid: PQE30 (QIAGEN) / Gene (production host): FBN1 / Production host: Escherichia coli (E. coli) / Strain (production host): NM554 (HIS TAG) / References: UniProt: P35555
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H-NOESY
121COSY
131TOCSY

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Sample preparation

Sample conditionspH: 6.5 / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
GE OMEGAGEOMEGA5001
Bruker AMBrukerAM6002

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1BRUNGERstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: F(NOE) < 165 KJ MOL-1 TORSION ANGLE CONSTRAINTS VIOLATED BY > 3 DEGREES
Conformers calculated total number: 200 / Conformers submitted total number: 22

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