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- PDB-4lxo: Crystal structure of 9,10Fn3-elegantin chimera -

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Basic information

Entry
Database: PDB / ID: 4lxo
TitleCrystal structure of 9,10Fn3-elegantin chimera
ComponentsFibronectin
KeywordsCELL ADHESION / fibronectin type III domain / cell binding / integrin alpha5beta1
Function / homology
Function and homology information


negative regulation of monocyte activation / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / Fibronectin matrix formation / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / neural crest cell migration involved in autonomic nervous system development / peptidase activator activity / fibrinogen complex / peptide cross-linking ...negative regulation of monocyte activation / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / Fibronectin matrix formation / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / neural crest cell migration involved in autonomic nervous system development / peptidase activator activity / fibrinogen complex / peptide cross-linking / integrin activation / ALK mutants bind TKIs / cell-substrate junction assembly / biological process involved in interaction with symbiont / proteoglycan binding / Molecules associated with elastic fibres / extracellular matrix structural constituent / MET activates PTK2 signaling / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / endodermal cell differentiation / GRB2:SOS provides linkage to MAPK signaling for Integrins / endoplasmic reticulum-Golgi intermediate compartment / Non-integrin membrane-ECM interactions / basement membrane / ECM proteoglycans / Integrin cell surface interactions / positive regulation of axon extension / collagen binding / Degradation of the extracellular matrix / Integrin signaling / regulation of ERK1 and ERK2 cascade / cell-matrix adhesion / substrate adhesion-dependent cell spreading / extracellular matrix / platelet alpha granule lumen / acute-phase response / integrin-mediated signaling pathway / Post-translational protein phosphorylation / Cell surface interactions at the vascular wall / wound healing / Signaling by high-kinase activity BRAF mutants / regulation of protein phosphorylation / MAP2K and MAPK activation / response to wounding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / GPER1 signaling / positive regulation of fibroblast proliferation / Signaling by BRAF and RAF1 fusions / Signaling by ALK fusions and activated point mutants / integrin binding / Platelet degranulation / heart development / heparin binding / nervous system development / regulation of cell shape / Interleukin-4 and Interleukin-13 signaling / protease binding / angiogenesis / collagen-containing extracellular matrix / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / apical plasma membrane / endoplasmic reticulum lumen / signaling receptor binding / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Fibronectin type I domain / : / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. ...Fibronectin type I domain / : / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Kringle-like fold / EGF-like domain signature 1. / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsChang, Y.S. / Shiu, J.H. / Chuang, W.J.
CitationJournal: To be Published
Title: Design, Structure Determination, and Biological Evaluation of Potent Integrin Alpha5beta1-Specific Antagonist Using the Ninth and Tenth Module of Fibronectin Type III Domain
Authors: Chang, Y.S. / Shiu, J.H. / Chuang, W.J.
History
DepositionJul 30, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibronectin
B: Fibronectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1034
Polymers42,0232
Non-polymers802
Water9,080504
1
A: Fibronectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0512
Polymers21,0111
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fibronectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0512
Polymers21,0111
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.115, 75.115, 175.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Fibronectin / FN / Cold-insoluble globulin / CIG / Anastellin / Ugl-Y1 / Ugl-Y2 / Ugl-Y3


Mass: 21011.369 Da / Num. of mol.: 2
Mutation: L1408P, V1490C, T1491R, G1492A, S1496N, A1498D, S1499C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FN1, FN / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 / References: UniProt: P02751
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 504 / Source method: isolated from a natural source / Formula: H2O

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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: 2.95 Å3/Da / Density % sol: 58.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.2M calcium acetate, 7%(w/v) PEG10000, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1,0000
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2011
Details: Vertically Collimating Premirror, Toroidal Focusing Mirror
RadiationMonochromator: LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
201
ReflectionResolution: 1.42→30 Å / Num. all: 97940 / Num. obs: 95355 / % possible obs: 97.36 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 7.8 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 49.4
Reflection shellResolution: 1.42→1.47 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 3.1 / Num. unique all: 10270 / % possible all: 91.74

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FNF

1fnf


Resolution: 1.42→29.4 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.56 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19305 4767 5 %RANDOM
Rwork0.1625 ---
obs0.16402 90292 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.404 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2--0.74 Å20 Å2
3----1.48 Å2
Refinement stepCycle: LAST / Resolution: 1.42→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2828 0 2 504 3334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222902
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.9573980
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3845366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1322.295122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34515428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3271528
X-RAY DIFFRACTIONr_chiral_restr0.1240.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0222248
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4561.51844
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.74623032
X-RAY DIFFRACTIONr_scbond_it4.79531058
X-RAY DIFFRACTIONr_scangle_it6.8884.5948
X-RAY DIFFRACTIONr_rigid_bond_restr2.47932902
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.42→1.497 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.257 657 -
Rwork0.216 13014 -
obs--99.72 %
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)
10.64620.14410.45040.14030.09271.2987-0.04930.00390.07040.0070.00990.0179-0.19460.01450.03940.07840.0119-0.00490.00610.00690.0359-18.4863.058-26.678
20.92290.15140.28990.5488-0.11630.84330.01250.065-0.09060.01390.0003-0.05060.03010.0762-0.01290.04230.01530.0190.01250.00140.0295-14.136-13.27-24.867
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1326 - 1509
2X-RAY DIFFRACTION1A1601
3X-RAY DIFFRACTION1A1701 - 1980
4X-RAY DIFFRACTION2B1326 - 1509
5X-RAY DIFFRACTION2B1601
6X-RAY DIFFRACTION2B1701 - 1924

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