[English] 日本語
Yorodumi
- PDB-5oyj: Crystal structure of VEGFR-2 domains 4-5 in complex with DARPin D4b -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5oyj
TitleCrystal structure of VEGFR-2 domains 4-5 in complex with DARPin D4b
Components
  • DARPin D4b
  • Vascular endothelial growth factor receptor 2
KeywordsSIGNALING PROTEIN / glycoprotein receptor kinase designed ankyrin repeat protein angiogenesis
Function / homology
Function and homology information


positive regulation of nitric oxide-cGMP mediated signal transduction / blood vessel endothelial cell differentiation / cellular response to hydrogen sulfide / regulation of bone development / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / Neurophilin interactions with VEGF and VEGFR / vascular endothelial growth factor binding / vascular endothelial growth factor receptor-2 signaling pathway / endothelium development / VEGF binds to VEGFR leading to receptor dimerization ...positive regulation of nitric oxide-cGMP mediated signal transduction / blood vessel endothelial cell differentiation / cellular response to hydrogen sulfide / regulation of bone development / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / Neurophilin interactions with VEGF and VEGFR / vascular endothelial growth factor binding / vascular endothelial growth factor receptor-2 signaling pathway / endothelium development / VEGF binds to VEGFR leading to receptor dimerization / endocardium development / vascular wound healing / regulation of hematopoietic progenitor cell differentiation / post-embryonic camera-type eye morphogenesis / lymph vessel development / mesenchymal cell proliferation / positive regulation of vasculogenesis / endothelial cell differentiation / positive regulation of BMP signaling pathway / surfactant homeostasis / cell migration involved in sprouting angiogenesis / epithelial cell maturation / positive regulation of positive chemotaxis / positive regulation of endothelial cell chemotaxis / anchoring junction / embryonic hemopoiesis / vascular endothelial growth factor signaling pathway / positive regulation of mesenchymal cell proliferation / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of mitochondrial fission / branching involved in blood vessel morphogenesis / lung alveolus development / positive regulation of stem cell proliferation / positive regulation of mitochondrial depolarization / growth factor binding / sorting endosome / regulation of MAPK cascade / semaphorin-plexin signaling pathway / positive regulation of macroautophagy / cellular response to vascular endothelial growth factor stimulus / positive regulation of focal adhesion assembly / cell fate commitment / positive regulation of blood vessel endothelial cell migration / Integrin cell surface interactions / vascular endothelial growth factor receptor signaling pathway / negative regulation of endothelial cell apoptotic process / vasculogenesis / peptidyl-tyrosine autophosphorylation / calcium ion homeostasis / coreceptor activity / ovarian follicle development / positive regulation of endothelial cell proliferation / transmembrane receptor protein tyrosine kinase activity / positive regulation of endothelial cell migration / cell surface receptor protein tyrosine kinase signaling pathway / VEGFR2 mediated cell proliferation / epithelial cell proliferation / stem cell proliferation / Hsp90 protein binding / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / VEGFA-VEGFR2 Pathway / positive regulation of angiogenesis / integrin binding / cell junction / cell migration / regulation of cell shape / positive regulation of protein phosphorylation / protein autophosphorylation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / protein tyrosine kinase activity / angiogenesis / negative regulation of neuron apoptotic process / early endosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / endosome / positive regulation of cell migration / cadherin binding / membrane raft / external side of plasma membrane / negative regulation of gene expression
Similarity search - Function
Vascular endothelial growth factor receptor 2 (VEGFR2) / VEGFR-2, transmembrane domain / : / : / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-like domain / VEGFR1-3, N-terminal Ig-like domain / VEGFR-1-like, immunoglobulin-like domain / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. ...Vascular endothelial growth factor receptor 2 (VEGFR2) / VEGFR-2, transmembrane domain / : / : / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-like domain / VEGFR1-3, N-terminal Ig-like domain / VEGFR-1-like, immunoglobulin-like domain / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin domain / Ankyrin repeat-containing domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Alpha Horseshoe / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
trehalose / ACETATE ION / CACODYLATE ION / Vascular endothelial growth factor receptor 2
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsPiscitelli, C.L. / Thieltges, K.M. / Markovic-Mueller, S. / Binz, H.K. / Ballmer-Hofer, K.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Switzerland
CitationJournal: Angiogenesis / Year: 2018
Title: Characterization of a drug-targetable allosteric site regulating vascular endothelial growth factor signaling.
Authors: Thieltges, K.M. / Avramovic, D. / Piscitelli, C.L. / Markovic-Mueller, S. / Binz, H.K. / Ballmer-Hofer, K.
History
DepositionSep 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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_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 / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: 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
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DARPin D4b
B: DARPin D4b
C: Vascular endothelial growth factor receptor 2
D: Vascular endothelial growth factor receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,56321
Polymers89,1864
Non-polymers4,37717
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8800 Å2
ΔGint-8 kcal/mol
Surface area40460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.489, 164.559, 70.759
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-610-

CAC

21C-754-

HOH

-
Components

-
Protein , 2 types, 4 molecules ABCD

#1: Protein DARPin D4b


Mass: 18339.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21 (bacteria)
#2: Protein Vascular endothelial growth factor receptor 2 / VEGFR-2 / Fetal liver kinase 1 / FLK-1 / Kinase insert domain receptor / KDR / Protein-tyrosine ...VEGFR-2 / Fetal liver kinase 1 / FLK-1 / Kinase insert domain receptor / KDR / Protein-tyrosine kinase receptor flk-1


Mass: 26253.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDR, FLK1, VEGFR2 / Cell line (production host): HEK-293 EBNA / Production host: Homo sapiens (human)
References: UniProt: P35968, receptor protein-tyrosine kinase

-
Sugars , 2 types, 10 molecules

#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE

-
Non-polymers , 5 types, 277 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.25 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.2 M calcium acetate monohydrate, 15% PEG 4000, 0.1 M sodium cacodylate pH 6.4, cryoprotected with 15% trehalose

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 28, 2016
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→55.9 Å / Num. obs: 52035 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 50.83 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.038 / Net I/σ(I): 10.7
Reflection shellResolution: 2.38→2.44 Å / Redundancy: 13 % / Rmerge(I) obs: 2.37 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3808 / CC1/2: 0.675 / Rpim(I) all: 0.68 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(dev_2722: ???)refinement
XDSdata reduction
Aimless0.5.26data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BSJ, 2QYJ

4bsj

2qyj


Resolution: 2.38→38.749 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.46
RfactorNum. reflection% reflectionSelection details
Rfree0.2288 2582 5.01 %random
Rwork0.1779 ---
obs0.1804 51496 98.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.38→38.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5915 0 279 270 6464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096390
X-RAY DIFFRACTIONf_angle_d1.068728
X-RAY DIFFRACTIONf_dihedral_angle_d18.1873764
X-RAY DIFFRACTIONf_chiral_restr0.061025
X-RAY DIFFRACTIONf_plane_restr0.0071109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.42580.41371330.36122616X-RAY DIFFRACTION97
2.4258-2.47530.3691320.35142643X-RAY DIFFRACTION97
2.4753-2.52910.40051410.33612634X-RAY DIFFRACTION96
2.5291-2.58790.3191450.29312584X-RAY DIFFRACTION97
2.5879-2.65270.31341450.2592660X-RAY DIFFRACTION98
2.6527-2.72440.30971370.25112703X-RAY DIFFRACTION99
2.7244-2.80450.28731650.23392663X-RAY DIFFRACTION99
2.8045-2.8950.26131470.22712717X-RAY DIFFRACTION100
2.895-2.99840.25331360.21652707X-RAY DIFFRACTION100
2.9984-3.11840.25891510.19492725X-RAY DIFFRACTION100
3.1184-3.26030.24521350.18942728X-RAY DIFFRACTION100
3.2603-3.43210.24831480.17472736X-RAY DIFFRACTION100
3.4321-3.6470.25921360.17432735X-RAY DIFFRACTION99
3.647-3.92830.18381710.14722730X-RAY DIFFRACTION100
3.9283-4.32310.16111180.12572782X-RAY DIFFRACTION100
4.3231-4.94760.17321370.11792786X-RAY DIFFRACTION100
4.9476-6.22930.1611610.14982818X-RAY DIFFRACTION100
6.2293-38.75360.24191440.17192947X-RAY DIFFRACTION99
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)
13.19812.6733.6762.72941.45119.5240.7612-0.65210.05130.4244-0.6460.32220.3526-0.9685-0.10680.5837-0.02980.14080.5287-0.03240.8327-44.1167-10.22-25.5509
23.59275.49591.96478.50543.02085.3598-0.54241.0074-0.4477-0.50020.7504-0.68690.85330.3911-0.18990.7498-0.03710.16380.44220.02480.7954-38.5606-13.7473-33.2823
33.54640.88710.49164.6285-0.66331.3237-0.1809-0.0489-0.56080.21240.16030.19070.0734-0.07980.0270.3625-0.02960.11770.3558-0.05130.3088-38.05265.0974-33.2674
46.53822.3432.17387.7285-1.47412.4355-0.32510.19120.2849-0.07710.16350.1343-0.3065-0.09630.10340.3043-0.05330.02970.44430.01120.2594-31.159420.8501-36.9936
55.52573.55845.22426.98383.35175.51160.10110.84790.5511-1.00590.30460.6539-0.2551-0.1327-0.29910.4718-0.0383-0.00180.54540.04150.456-25.134223.3834-41.6465
68.61-4.9330.13643.31220.89962.386-0.0493-0.08480.65381.9052-0.39050.98250.3842-1.07740.41770.9195-0.10380.10590.75190.00720.5755-79.045327.6947-13.1695
75.4055.11-5.09495.8239-5.74075.72810.5688-1.7353-0.15281.9038-0.14740.12910.6942-0.0454-0.39271.452-0.06780.05931.21180.1430.8283-73.922930.4431-5.5252
85.00910.2090.11883.6918-1.3569.50770.2401-0.575-0.88111.27330.15570.92090.3795-0.7051-0.33480.7031-0.00760.0010.4480.18270.7803-73.207426.3924-17.8971
92.78860.1768-2.87793.5873-4.98259.41270.1592-1.1683-0.23612.3169-0.5356-1.01170.50190.79060.23120.9245-0.0027-0.2580.59930.12490.6209-64.664428.1226-10.2415
106.9924-1.5840.39765.44740.7287.670.5788-0.0013-1.2071.1914-0.15330.52710.60520.2998-0.30920.6081-0.0868-0.18450.40020.1410.9624-68.32922.597-25.3296
115.0898-3.53312.24813.6922-2.97922.7481-0.1301-0.50240.26620.9036-0.01130.01090.00290.13090.06370.6301-0.0285-0.18940.44860.04250.8875-60.976232.4239-21.6049
129.2368-1.44015.90345.6864-0.06593.91780.32690.0703-1.14670.19890.5316-0.7999-0.08890.0218-0.95260.6553-0.0171-0.16710.47050.0220.9099-61.206424.4329-29.9956
136.07-2.1017-2.10626.8572-2.18827.0452-0.1169-0.1994-0.23860.20360.3015-1.28340.04750.1969-0.16990.3523-0.0059-0.08060.2394-0.0980.7539-56.220135.3214-29.5647
146.0925-1.2571-0.28568.8888-0.62756.55390.04820.6615-0.9035-0.02370.4923-1.63340.3520.396-0.48450.4757-0.05350.00870.5921-0.23391.043-57.221827.4992-39.9864
156.5993-3.9878-3.63612.92781.67442.5560.27750.7321-1.0671-0.93390.4261-1.96340.3101-0.3137-0.66350.6222-0.04390.08060.7369-0.25540.9635-56.850438.6336-41.5932
164.2541-3.90261.35334.0743-0.98398.47730.67630.30511.544-0.8037-0.3261-2.5584-0.60581.559-0.27740.6302-0.14620.08460.9056-0.1441.197-48.641539.2224-37.1898
173.37521.5879-1.9422.81411.46827.6813-0.4422-1.29391.28510.30770.8569-0.95320.35221.0376-0.39160.44770.0185-0.04350.5318-0.1310.4799-5.791231.3103-33.7375
186.1753-3.9357-2.12215.0821.42561.90910.11860.13510.6001-0.36090.055-0.0722-0.3623-0.1313-0.15580.40970.0243-0.00650.36680.06530.4557-20.457441.9012-39.9675
198.3675-6.0976-6.11064.77284.91795.5999-0.1188-0.15560.27030.03060.1676-0.0530.0350.03930.04870.3293-0.0290.02060.3484-0.0110.4533-20.848935.3267-36.6101
204.9805-3.6984-3.59195.60083.65693.71921.27721.46630.952-1.3797-0.9106-0.6659-0.7246-0.06810.02470.60380.02170.11220.59710.09220.6648-45.888864.085-30.9266
214.0838-2.0753-0.96067.27282.36731.1384-0.26180.1114-0.1030.58170.268-0.0330.23830.04910.0350.45150.02370.0330.4859-0.01790.4588-49.70565.4499-20.8883
222.7199-1.6848-0.93459.5096-0.28672.1942-0.2505-0.40990.01510.32540.1564-0.9018-0.23420.1860.21720.4596-0.04070.03250.5478-0.04260.6408-44.412674.4872-19.1891
233.2685-1.6578-0.64033.69271.45261.839-0.1346-0.1311-0.55380.97950.15950.00950.20930.0721-0.00440.5311-0.00110.03060.4128-0.00690.5888-53.046259.1993-19.8968
241.05811.17470.97272.55731.04372.4728-0.0740.10350.11890.2847-0.13150.1587-0.09180.0933-0.06660.3666-0.00730.04810.4119-0.03290.455-50.001969.1277-23.4605
255.738-0.0964-2.4223.01470.77226.09910.071-0.3264-0.28580.44380.0368-0.3740.17370.3582-0.11570.50610.0267-0.03310.3899-0.00030.3487-21.38298.5636-23.1794
260.60820.6867-1.80412.1474-3.59257.1072-0.44350.4397-0.4911-0.5165-0.11920.47350.887-0.38030.62320.6859-0.11010.00520.7312-0.08190.5074-44.28048.375417.2493
272.1653-0.09-2.45553.20550.05866.49170.16340.280.2954-0.39690.02120.6777-0.0083-0.2481-0.17010.4833-0.041-0.08090.69240.01030.4835-45.240716.39314.0709
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 35 )
3X-RAY DIFFRACTION3chain 'A' and (resid 36 through 125 )
4X-RAY DIFFRACTION4chain 'A' and (resid 126 through 155 )
5X-RAY DIFFRACTION5chain 'A' and (resid 156 through 169 )
6X-RAY DIFFRACTION6chain 'B' and (resid 13 through 23 )
7X-RAY DIFFRACTION7chain 'B' and (resid 24 through 35 )
8X-RAY DIFFRACTION8chain 'B' and (resid 36 through 59 )
9X-RAY DIFFRACTION9chain 'B' and (resid 60 through 69 )
10X-RAY DIFFRACTION10chain 'B' and (resid 70 through 82 )
11X-RAY DIFFRACTION11chain 'B' and (resid 83 through 101 )
12X-RAY DIFFRACTION12chain 'B' and (resid 102 through 115 )
13X-RAY DIFFRACTION13chain 'B' and (resid 116 through 135 )
14X-RAY DIFFRACTION14chain 'B' and (resid 136 through 148 )
15X-RAY DIFFRACTION15chain 'B' and (resid 149 through 158 )
16X-RAY DIFFRACTION16chain 'B' and (resid 159 through 169 )
17X-RAY DIFFRACTION17chain 'C' and (resid 322 through 338 )
18X-RAY DIFFRACTION18chain 'C' and (resid 339 through 389 )
19X-RAY DIFFRACTION19chain 'C' and (resid 390 through 418 )
20X-RAY DIFFRACTION20chain 'C' and (resid 419 through 433 )
21X-RAY DIFFRACTION21chain 'C' and (resid 434 through 465 )
22X-RAY DIFFRACTION22chain 'C' and (resid 466 through 493 )
23X-RAY DIFFRACTION23chain 'C' and (resid 494 through 525 )
24X-RAY DIFFRACTION24chain 'C' and (resid 526 through 552 )
25X-RAY DIFFRACTION25chain 'D' and (resid 322 through 418 )
26X-RAY DIFFRACTION26chain 'D' and (resid 419 through 440 )
27X-RAY DIFFRACTION27chain 'D' and (resid 441 through 553 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more