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- PDB-3gxe: Complex of a Low Affinity Collagen Site with the Fibronectin 8-9F... -

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Basic information

Entry
Database: PDB / ID: 3gxe
TitleComplex of a Low Affinity Collagen Site with the Fibronectin 8-9FnI Domain Pair
Components
  • (Collagen alpha-1(I) ...) x 2
  • Fibronectin
KeywordsCELL ADHESION / protein-peptide complex
Function / homology
Function and homology information


collagen type I trimer / cellular response to vitamin E / tooth mineralization / cellular response to fluoride / Anchoring fibril formation / intramembranous ossification / Crosslinking of collagen fibrils / collagen biosynthetic process / negative regulation of monocyte activation / Collagen chain trimerization ...collagen type I trimer / cellular response to vitamin E / tooth mineralization / cellular response to fluoride / Anchoring fibril formation / intramembranous ossification / Crosslinking of collagen fibrils / collagen biosynthetic process / negative regulation of monocyte activation / Collagen chain trimerization / Defective VWF binding to collagen type I / platelet-derived growth factor binding / bone trabecula formation / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / extracellular matrix structural constituent conferring tensile strength / negative regulation of transforming growth factor beta production / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Fibronectin matrix formation / calcium-independent cell-matrix adhesion / embryonic skeletal system development / neural crest cell migration involved in autonomic nervous system development / cartilage development involved in endochondral bone morphogenesis / skin morphogenesis / fibrinogen complex / Collagen biosynthesis and modifying enzymes / peptide cross-linking / collagen-activated tyrosine kinase receptor signaling pathway / endochondral ossification / Platelet Adhesion to exposed collagen / integrin activation / ALK mutants bind TKIs / cell-substrate junction assembly / collagen fibril organization / proteoglycan binding / response to steroid hormone / face morphogenesis / Assembly of collagen fibrils and other multimeric structures / extracellular matrix structural constituent / MET activates PTK2 signaling / Molecules associated with elastic fibres / Scavenging by Class A Receptors / peptidase activator activity / biological process involved in interaction with symbiont / Syndecan interactions / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / blood vessel development / response to muscle activity / Platelet Aggregation (Plug Formation) / RUNX2 regulates osteoblast differentiation / endoplasmic reticulum-Golgi intermediate compartment / endodermal cell differentiation / Collagen degradation / regulation of protein phosphorylation / GRB2:SOS provides linkage to MAPK signaling for Integrins / basement membrane / Non-integrin membrane-ECM interactions / negative regulation of cell-substrate adhesion / response to hyperoxia / ECM proteoglycans / response to cAMP / Integrin cell surface interactions / protein localization to nucleus / cellular response to transforming growth factor beta stimulus / positive regulation of epithelial to mesenchymal transition / endothelial cell migration / regulation of ERK1 and ERK2 cascade / positive regulation of axon extension / collagen binding / GPVI-mediated activation cascade / Degradation of the extracellular matrix / cellular response to retinoic acid / cellular response to fibroblast growth factor stimulus / Integrin signaling / visual perception / extracellular matrix / substrate adhesion-dependent cell spreading / platelet alpha granule lumen / secretory granule / cellular response to epidermal growth factor stimulus / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / acute-phase response / Cell surface interactions at the vascular wall / integrin-mediated signaling pathway / skeletal system development / Post-translational protein phosphorylation / cellular response to amino acid stimulus / wound healing / response to hydrogen peroxide / cellular response to glucose stimulus / sensory perception of sound / cellular response to mechanical stimulus / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / response to insulin
Similarity search - Function
Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / : / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain ...Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / : / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / : / von Willebrand factor type C domain / Complement Module, domain 1 / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / 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 / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / 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
Collagen alpha-1(I) chain / Fibronectin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsSladek, B. / Campbell, I.D. / Vakonakis, I.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural analysis of collagen type I interactions with human fibronectin reveals a cooperative binding mode
Authors: Erat, M.C. / Sladek, B. / Campbell, I.D. / Vakonakis, I.
History
DepositionApr 2, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 15, 2013Group: Database references / Refinement description
Revision 1.3Jan 29, 2014Group: Database references
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / 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 / _struct_ref_seq_dif.details
Revision 1.6Nov 1, 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
Revision 1.7Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Fibronectin
F: Collagen alpha-1(I) chain
A: Fibronectin
E: Collagen alpha-1(I) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8807
Polymers26,3454
Non-polymers5353
Water79344
1
B: Fibronectin
F: Collagen alpha-1(I) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3943
Polymers13,1732
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Fibronectin
E: Collagen alpha-1(I) chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4864
Polymers13,1732
Non-polymers3132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.570, 56.570, 152.661
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
11B-612-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and not (resseq 521:522 or resseq 546:552 or...
21(chain B and not (resseq 521:522 or resseq 546:552 or...
12chain E and resseq 260:267 and not (resname HZP or resname HYP)
22chain F and resseq 260:267 and not (resname HZP 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
11ASPASPLEULEUAC516 - 6021 - 87
21ASPASPTHRTHRBA516 - 6041 - 89
12GLYGLYLEULEUED254 - 2731 - 20
22GLYGLYPHEPHEFB260 - 2707 - 17

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.994176, 0.074947, 0.077439), (-0.081142, 0.04768, 0.995562), (0.070922, -0.996047, 0.053483)17.5567, 4.24073, -49.605099
2given(0.994044, 0.052047, 0.095744), (-0.096477, 0.011747, 0.995266), (0.050676, -0.998576, 0.016699)17.817499, 4.11278, -49.961201

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Components

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Collagen alpha-1(I) ... , 2 types, 2 molecules FE

#2: Protein/peptide Collagen alpha-1(I) chain / Alpha-1 type I collagen


Mass: 2280.543 Da / Num. of mol.: 1 / Fragment: ColI.260, UNP residues 254-275 / Source method: obtained synthetically / Details: Standard peptide synthesis / References: UniProt: P02452
#3: Protein/peptide Collagen alpha-1(I) chain / Alpha-1 type I collagen


Mass: 2280.543 Da / Num. of mol.: 1 / Fragment: ColI.260, UNP residues 254-275 / Source method: obtained synthetically / Details: Standard peptide synthesis / References: UniProt: P02452

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Protein / Sugars , 2 types, 4 molecules BA

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


Mass: 10891.985 Da / Num. of mol.: 2 / Fragment: 8-9FnI, UNP residues 516-608 / Mutation: N528Q, R534K
Source method: isolated from a genetically manipulated source
Details: Gene fragment integrated in the AOX1 locus / Source: (gene. exp.) Homo sapiens (human) / Gene: FN / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P02751
#4: 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

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Non-polymers , 2 types, 45 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.68 Å3/Da / Density % sol: 54.05 % / Mosaicity: 0.841 °
Crystal growTemperature: 293.1 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 4.3M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293.1K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2009 / Details: cylindrical grazing incidence mirror
RadiationMonochromator: silicon monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.558→46.676 Å / Num. all: 16850 / Num. obs: 16804 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 14.5
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 2.4 / Num. measured all: 8589 / Num. unique all: 2462 / Rsym value: 0.442 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 39.27 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.8 Å49.46 Å
Translation2.8 Å49.46 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASERphasing
PHENIX2009_02_15_2320_3refinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3EJH, Chain A and part of chain E

3ejh


Resolution: 2.6→46.648 Å / Occupancy max: 1 / Occupancy min: 0.43 / FOM work R set: 0.798 / SU ML: 0.99 / Isotropic thermal model: TLS / σ(F): 0.19 / Stereochemistry target values: ML
Details: The SF file contains Friedel pairs under I/F_plus and I/F_minus column.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1242 7.39 %R-free at same indices as Mr model
Rwork0.219 ---
all0.223 16796 --
obs0.223 16796 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.82 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso max: 176.72 Å2 / Biso mean: 57.63 Å2 / Biso min: 19.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.666 Å2-0 Å20 Å2
2--2.666 Å20 Å2
3----5.332 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 0 34 44 1714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031733
X-RAY DIFFRACTIONf_angle_d0.6832319
X-RAY DIFFRACTIONf_chiral_restr0.046221
X-RAY DIFFRACTIONf_plane_restr0.002301
X-RAY DIFFRACTIONf_dihedral_angle_d12.613612
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A493X-RAY DIFFRACTIONPOSITIONAL
12B493X-RAY DIFFRACTIONPOSITIONAL0.021
21E47X-RAY DIFFRACTIONPOSITIONAL
22F47X-RAY DIFFRACTIONPOSITIONAL0.014
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.6-2.7040.3791590.319174419031903100
2.704-2.8270.3661240.281174218661866100
2.827-2.9770.341340.269172518591859100
2.977-3.1630.3251450.234171318581858100
3.163-3.4070.3051380.214171718551855100
3.407-3.750.221360.187174918851885100
3.75-4.2920.2451440.173171018541854100
4.292-5.4060.1991350.17417131848184899
5.406-46.6550.2421270.20717411868186899
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)
11.1606-0.23250.45833.8604-1.64620.8335-0.1904-0.06580.0444-0.38040.2892-0.32590.228-0.1721-0.1110.1501-0.10310.06590.3521-0.02650.126743.805-26.9047-33.715
21.16042.1081-0.66184.7072-2.35052.53960.0248-0.2539-0.28190.467-0.3152-1.13820.0099-0.11130.24410.2891-0.0706-0.09840.1450.1250.281856.2241-2.6138-34.7014
32.741-0.2616-2.16812.84821.92392.75910.06210.4517-0.1216-0.2889-0.1413-0.2182-0.4857-0.10.10460.15110.0414-0.02020.35540.0930.108629.8398-15.1919-27.899
41.485-0.8987-0.16651.0131-0.4552.3307-0.03510.06170.0666-0.0125-0.124-0.08390.0785-0.3280.10440.14170.0511-0.02320.11020.00580.109740.8892-11.8395-2.7806
50.50011.45460.27265.31681.25670.80210.06690.166-0.0924-0.5742-0.3619-0.367-0.1873-0.40020.16490.0785-0.00090.0140.2879-0.08890.106636.3308-21.5332-33.9141
62.27880.8924-1.1811.9203-0.41092.9604-0.15690.1562-0.1555-0.39420.4693-0.28090.0236-0.86290.0710.20060.00670.07490.410.14320.18121.9467-15.9345-25.3542
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 516:558) or (chain A and resseq 1)
2X-RAY DIFFRACTION2chain A and resseq 559:602
3X-RAY DIFFRACTION3(chain B and resseq 516:558) or (chain B and resseq 1)
4X-RAY DIFFRACTION4chain B and resseq 559:604
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F

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