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- PDB-3ejh: Crystal Structure of the Fibronectin 8-9FnI Domain Pair in Comple... -

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Basic information

Entry
Database: PDB / ID: 3ejh
TitleCrystal Structure of the Fibronectin 8-9FnI Domain Pair in Complex with a Type-I Collagen Peptide
Components
  • Collagen type-I a1 chain
  • Fibronectin
KeywordsCELL ADHESION / fibronectin / collagen / protein complex / collagenase site / Acute phase / Disease mutation / Extracellular matrix / Glycoprotein / Heparin-binding / Phosphoprotein / Pyrrolidone carboxylic acid / Secreted / Sulfation
Function / homology
Function and homology information


negative regulation of monocyte activation / negative regulation of transforming growth factor beta production / Extracellular matrix organization / Fibronectin matrix formation / calcium-independent cell-matrix adhesion / 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 / negative regulation of transforming growth factor beta production / Extracellular matrix organization / Fibronectin matrix formation / calcium-independent cell-matrix adhesion / 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 / proteoglycan binding / biological process involved in interaction with symbiont / extracellular matrix structural constituent / Molecules associated with elastic fibres / MET activates PTK2 signaling / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / response to muscle activity / endoplasmic reticulum-Golgi intermediate compartment / endodermal cell differentiation / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of protein phosphorylation / basement membrane / Non-integrin membrane-ECM interactions / ECM proteoglycans / Integrin cell surface interactions / positive regulation of axon extension / endothelial cell migration / regulation of ERK1 and ERK2 cascade / collagen binding / Degradation of the extracellular matrix / Integrin signaling / extracellular matrix / substrate adhesion-dependent cell spreading / platelet alpha granule lumen / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / acute-phase response / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / wound healing / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / response to wounding / positive regulation of fibroblast proliferation / 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 / Signaling by BRAF and RAF1 fusions / Signaling by ALK fusions and activated point mutants / integrin binding / GPER1 signaling / Platelet degranulation / nervous system development / heparin binding / regulation of cell shape / heart development / protease binding / : / Interleukin-4 and Interleukin-13 signaling / angiogenesis / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / apical plasma membrane / receptor ligand activity / 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 / : / Complement Module, domain 1 / Complement Module; domain 1 / Fibronectin type II domain / Fibronectin type II domain superfamily ...Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / : / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsErat, M.C. / Lowe, E.D. / Campbell, I.D. / Vakonakis, I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Identification and structural analysis of type I collagen sites in complex with fibronectin fragments.
Authors: Erat, M.C. / Slatter, D.A. / Lowe, E.D. / Millard, C.J. / Farndale, R.W. / Campbell, I.D. / Vakonakis, I.
History
DepositionSep 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 20, 2021Group: Database references / Source and taxonomy / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibronectin
E: Collagen type-I a1 chain
B: Fibronectin
F: Collagen type-I a1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1307
Polymers26,5954
Non-polymers5353
Water1,892105
1
A: Fibronectin
E: Collagen type-I a1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5193
Polymers13,2982
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fibronectin
F: Collagen type-I a1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6114
Polymers13,2982
Non-polymers3132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.840, 56.840, 150.220
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-650-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and not (resseq 546:552 or resseq 558 or...
21(chain B and not (resseq 546:552 or resseq 558 or...
12chain E and resseq 961:973 and not (resname HXP or resname HYP)
22chain F and resseq 961:973 and not (resname HXP or resname HYP)

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPPROPROAA516 - 6061 - 91
21ASPASPLEULEUBC516 - 6021 - 87
12VALVALGLYGLYEB960 - 9745 - 19
22GLYGLYTYRTYRFD956 - 9781 - 23

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.261943, 0.313324, 0.912805), (0.476324, 0.780628, -0.404642), (-0.839346, 0.540784, 0.055237)-25.460899, 0.766322, -25.1625
2given(0.247755, 0.367001, 0.89662), (0.482008, 0.756112, -0.442677), (-0.840408, 0.541854, 0.010433)-27.2542, 1.15435, -25.5905

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Components

#1: Protein Fibronectin / FN / Cold-insoluble globulin / CIG


Mass: 10891.985 Da / Num. of mol.: 2 / Fragment: 8-9FnI / Mutation: N528Q, R534K
Source method: isolated from a genetically manipulated source
Details: Integration in the AOX1 locus / Source: (gene. exp.) Homo sapiens (human) / Gene: FN1, FN / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P02751
#2: Protein/peptide Collagen type-I a1 chain


Mass: 2405.651 Da / Num. of mol.: 2 / Fragment: collagenase site C-terminal peptide / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human) type-I collagen a1 chain.
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2.5 M NaCl, 0.1 M BisTris pH 6.5 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 28, 2008
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2→49.225 Å / Num. obs: 19940 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 40.9 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 6.023
Reflection shellResolution: 2→2.1 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 1.2 / Num. measured all: 20451 / Num. unique all: 2872 / Rsym value: 0.571 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
PHASERphasing
RefinementStarting model: PDB ENTRIES 2CG6, 2CG7

2cg6

2cg7


Resolution: 2.1→49.225 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.828 / SU ML: 0.33 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.4 / Stereochemistry target values: ML / Details: One TLS group per FnI domain and peptide chain
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1229 7.26 %RAMDOM
Rwork0.209 ---
obs0.211 17126 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.312 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso max: 144.75 Å2 / Biso mean: 52.401 Å2 / Biso min: 20.1 Å2
Baniso -1Baniso -2Baniso -3
1-4.431 Å2-0 Å2-0 Å2
2--4.431 Å2-0 Å2
3----8.861 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1737 0 34 105 1876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081916
X-RAY DIFFRACTIONf_angle_d1.2972579
X-RAY DIFFRACTIONf_chiral_restr0.081247
X-RAY DIFFRACTIONf_plane_restr0.004339
X-RAY DIFFRACTIONf_dihedral_angle_d17.76682
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A477X-RAY DIFFRACTIONPOSITIONAL
12B477X-RAY DIFFRACTIONPOSITIONAL0.108
21E71X-RAY DIFFRACTIONPOSITIONAL
22F71X-RAY DIFFRACTIONPOSITIONAL0.053
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.1-2.1460.2761360.235180319391803100
2.146-2.1960.2791470.226186420111864100
2.196-2.250.3031470.234180819551808100
2.25-2.3110.2951480.232184119891841100
2.311-2.3790.3021440.247182519691825100
2.379-2.4560.3241440.247185720011857100
2.456-2.5440.3181360.236180819441808100
2.544-2.6460.3011470.244184519921845100
2.646-2.7660.2421380.223183119691831100
2.766-2.9120.2831460.214187120171871100
2.912-3.0950.3091380.234183019681830100
3.095-3.3330.2731450.201183719821837100
3.333-3.6690.1821480.184183919871839100
3.669-4.1990.171520.166181819701818100
4.199-5.290.2021430.166184019831840100
5.29-49.2380.2241380.19718171955181798
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)
12.54451.6166-0.96212.075-0.24910.7547-0.13070.16390.3137-0.40530.20660.1369-0.1953-0.3866-0.04370.2446-0.0348-0.07610.32520.00770.2801-28.223518.3287-2.6364
21.05881.3970.08362.2181-0.03970.61330.32340.11930.30050.5483-0.33710.15290.2519-0.11340.00250.2097-0.0720.04430.2629-0.0670.2604-26.468230.861423.086
32.46021.99970.1434-1.95790.44252.25440.03370.1807-0.0656-0.0794-0.0197-0.26580.42850.0835-0.01490.3440.0630.00310.10880.01080.2934-10.990524.6195-8.9458
43.0902-5.00611.77875.9771-1.02550.3359-0.6949-0.62030.65590.08530.1408-0.1602-0.6814-0.51030.5790.40130.2205-0.21640.2936-0.0430.6233-26.030647.4004-9.2038
51.20510.8031.38550.59631.5481.9948-0.2487-0.11660.25390.1447-0.45820.10180.998-1.22370.61110.3761-0.1177-0.03330.4296-0.00250.3401-31.292510.32372.0042
62.0260.1451-0.51415.07611.34621.2189-0.03630.51250.28310.26330.1525-0.64040.1609-0.1359-0.12920.3262-0.08380.10930.21410.00970.2425-21.331520.6247-9.0467
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A516 - 558
2X-RAY DIFFRACTION2A559 - 606
3X-RAY DIFFRACTION3B516 - 558
4X-RAY DIFFRACTION4B559 - 602
5X-RAY DIFFRACTION5E960 - 974
6X-RAY DIFFRACTION6F956 - 978

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