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- PDB-3m7p: Fibronectin fragment -

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Basic information

Entry
Database: PDB / ID: 3m7p
TitleFibronectin fragment
ComponentsFN1 protein
KeywordsCELL ADHESION / fibronectin / extracellular matrix / modular protein / zinc binding / dimer / conformational change
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 / MET activates PTK2 signaling / extracellular matrix structural constituent / 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 / substrate adhesion-dependent cell spreading / regulation of ERK1 and ERK2 cascade / cell-matrix adhesion / extracellular matrix / platelet alpha granule lumen / acute-phase response / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / regulation of protein phosphorylation / Signaling by high-kinase activity BRAF mutants / wound healing / MAP2K and MAPK activation / response to wounding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / GPER1 signaling / Signaling downstream of RAS mutants / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Signaling by BRAF and RAF1 fusions / positive regulation of fibroblast proliferation / Signaling by ALK fusions and activated point mutants / integrin binding / Platelet degranulation / nervous system development / heparin binding / heart development / regulation of cell shape / angiogenesis / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / protease binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / blood microparticle / 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 II, collagen-binding / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Seminal Fluid Protein PDC-109 (Domain B) / Complement Module, domain 1 / Complement Module; domain 1 / Fibronectin type II domain ...Fibronectin, type II, collagen-binding / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Seminal Fluid Protein PDC-109 (Domain B) / Complement Module, domain 1 / Complement Module; domain 1 / 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 / Fibronectin type III domain / EGF-like domain signature 1. / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Ribbon / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
Fibronectin / Fibronectin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsGraille, M. / Pagano, M. / Rose, T. / Reboud Ravaux, M. / van Tilbeurgh, H.
CitationJournal: Structure / Year: 2010
Title: Zinc Induces Structural Reorganization of Gelatin Binding Domain from Human Fibronectin and Affects Collagen Binding
Authors: Graille, M. / Pagano, M. / Rose, T. / Reboud Ravaux, M. / van Tilbeurgh, H.
History
DepositionMar 17, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FN1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,33013
Polymers35,1151
Non-polymers2,21512
Water1,11762
1
A: FN1 protein
hetero molecules

A: FN1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,65926
Polymers70,2302
Non-polymers4,43024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3960 Å2
ΔGint-20 kcal/mol
Surface area29180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.789, 124.789, 60.649
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein FN1 protein


Mass: 35114.773 Da / Num. of mol.: 1 / Fragment: Gelatin binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Purchased from Sigma-Aldrich / References: UniProt: B7ZLE5, UniProt: P02751*PLUS
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 3.88 Å3/Da / Density % sol: 68.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25-30% PEG 550 MME, 0.1M MES, 30-50mM ZnSO4, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 21, 2006
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 20851 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 66.84 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 9
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 1.2 / Rsym value: 0.621 / % possible all: 96.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
BUSTER2.8.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→19.87 Å / Cor.coef. Fo:Fc: 0.9344 / Cor.coef. Fo:Fc free: 0.9303 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2194 955 5.17 %RANDOM
Rwork0.1942 ---
all0.1955 20851 --
obs0.1955 18481 --
Displacement parametersBiso mean: 60.77 Å2
Baniso -1Baniso -2Baniso -3
1-3.8598 Å20 Å20 Å2
2--3.8598 Å20 Å2
3----7.7196 Å2
Refine analyzeLuzzati coordinate error obs: 0.314 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2393 0 75 62 2530
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012525HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.223416HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d823SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes77HARMONIC2
X-RAY DIFFRACTIONt_gen_planes366HARMONIC5
X-RAY DIFFRACTIONt_it2525HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.42
X-RAY DIFFRACTIONt_other_torsion22.37
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion318SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2661SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.65 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2822 176 5.9 %
Rwork0.2234 2808 -
obs-2984 -

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