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- PDB-4d90: Crystal Structure of Del-1 EGF domains -

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Basic information

Entry
Database: PDB / ID: 4d90
TitleCrystal Structure of Del-1 EGF domains
ComponentsEGF-like repeat and discoidin I-like domain-containing protein 3
KeywordsCELL ADHESION / RGD finger / innate immunity / extracellular matrix protein
Function / homology
Function and homology information


multicellular organism development / positive regulation of cell-substrate adhesion / extracellular vesicle / integrin binding / collagen-containing extracellular matrix / cell adhesion / calcium ion binding / extracellular exosome
Similarity search - Function
: / EGF-like, conserved site / Human growth factor-like EGF / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Laminin ...: / EGF-like, conserved site / Human growth factor-like EGF / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Laminin / Laminin / EGF-like domain / 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. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Galactose-binding-like domain superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
alpha-L-fucopyranose / 2-acetamido-2-deoxy-beta-D-galactopyranose / EGF-like repeat and discoidin I-like domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.601 Å
AuthorsChen, Q. / Schurpf, T. / Springer, T. / Wang, J.
CitationJournal: Faseb J. / Year: 2012
Title: The RGD finger of Del-1 is a unique structural feature critical for integrin binding.
Authors: Schurpf, T. / Chen, Q. / Liu, J.H. / Wang, R. / Springer, T.A. / Wang, J.H.
History
DepositionJan 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jul 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 / pdbx_struct_conn_angle / 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 / _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.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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EGF-like repeat and discoidin I-like domain-containing protein 3
B: EGF-like repeat and discoidin I-like domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,77710
Polymers30,4832
Non-polymers1,2938
Water90150
1
A: EGF-like repeat and discoidin I-like domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8885
Polymers15,2421
Non-polymers6474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: EGF-like repeat and discoidin I-like domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8885
Polymers15,2421
Non-polymers6474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint7 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.680, 82.680, 56.422
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein EGF-like repeat and discoidin I-like domain-containing protein 3 / Developmentally-regulated endothelial cell locus 1 protein / Integrin-binding protein DEL1


Mass: 15241.721 Da / Num. of mol.: 2 / Fragment: EGF domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: del-1, DEL1, EDIL3 / Plasmid: pLEXm / Cell line (production host): 293 GnTI(-) / Production host: HOMO SAPIENS (human) / References: UniProt: O43854

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Sugars , 3 types, 6 molecules

#2: Sugar ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#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: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 52 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 50 / 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: 3.65 Å3/Da / Density % sol: 66.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100 mM sodium acetate, 30% PEG 4000, 200 mM ammonium acetate, pH 4.6, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C10.9794
SYNCHROTRONAPS 19-ID20.9794
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDMar 7, 2010
ADSC QUANTUM 3152CCDJul 8, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Cryo-cooled Si(III) double crystalSINGLE WAVELENGTHMx-ray1
2Rosenbaum-Rock high-resolution double crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 13256 / Num. obs: 13233 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 51 Å2 / Rmerge(I) obs: 0.072 / Χ2: 1.047 / Net I/σ(I): 18
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.665.50.7778930.9891,2100
2.66-2.735.60.6258891.0711,2100
2.73-2.85.60.5258781.0931,2100
2.8-2.885.60.4018601.0951,2100
2.88-2.985.60.3169001.0421,2100
2.98-3.085.60.2788871.0951,2100
3.08-3.215.60.2038691.0821,2100
3.21-3.355.60.1448781.0671,2100
3.35-3.535.60.1049091.081,2100
3.53-3.755.60.0928791.0591,2100
3.75-4.045.50.0738811.0161,2100
4.04-4.455.50.0758670.9991,2100
4.45-5.095.50.0678840.9971,2100
5.09-6.415.40.0528950.9981,299.9
6.41-505.60.0468871.0131,299.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2VJ3

2vj3


Resolution: 2.601→44.317 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8276 / SU ML: 0.27 / σ(F): 1.97 / Phase error: 24.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2589 651 4.92 %random
Rwork0.2044 ---
obs0.207 13233 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.781 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 150.54 Å2 / Biso mean: 71.973 Å2 / Biso min: 32.72 Å2
Baniso -1Baniso -2Baniso -3
1-8.8646 Å2-0 Å2-0 Å2
2--8.8646 Å2-0 Å2
3----17.7292 Å2
Refinement stepCycle: LAST / Resolution: 2.601→44.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1866 0 78 50 1994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012012
X-RAY DIFFRACTIONf_angle_d1.462710
X-RAY DIFFRACTIONf_chiral_restr0.1289
X-RAY DIFFRACTIONf_plane_restr0.008373
X-RAY DIFFRACTIONf_dihedral_angle_d16.633746
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6014-2.80220.29941150.253225412656
2.8022-3.08420.27481470.219824852632
3.0842-3.53030.2531400.208625172657
3.5303-4.44710.25911200.18425152635
4.4471-44.32320.24881290.203625242653

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