[English] 日本語
Yorodumi
- PDB-4m4r: Epha4 ectodomain complex with ephrin a5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4m4r
TitleEpha4 ectodomain complex with ephrin a5
Components
  • Ephrin type-A receptor 4
  • Ephrin-A5
KeywordsTRANSFERASE / eph receptor ephrin complex
Function / homology
Function and homology information


neurotrophin TRKC receptor binding / neurotrophin TRKB receptor binding / DH domain binding / neuron projection fasciculation / : / negative regulation of proteolysis involved in protein catabolic process / corticospinal tract morphogenesis / regulation of astrocyte differentiation / neuron projection guidance / nephric duct morphogenesis ...neurotrophin TRKC receptor binding / neurotrophin TRKB receptor binding / DH domain binding / neuron projection fasciculation / : / negative regulation of proteolysis involved in protein catabolic process / corticospinal tract morphogenesis / regulation of astrocyte differentiation / neuron projection guidance / nephric duct morphogenesis / fasciculation of sensory neuron axon / fasciculation of motor neuron axon / synapse pruning / negative regulation of substrate adhesion-dependent cell spreading / negative regulation of cellular response to hypoxia / negative regulation of axon regeneration / transmembrane-ephrin receptor activity / glial cell migration / positive regulation of amyloid precursor protein catabolic process / synaptic membrane adhesion / PH domain binding / regulation of modification of synaptic structure / GPI-linked ephrin receptor activity / regulation of synapse pruning / collateral sprouting / cellular response to follicle-stimulating hormone stimulus / regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of collateral sprouting / adherens junction organization / neurotrophin TRKA receptor binding / positive regulation of dendrite morphogenesis / transmembrane receptor protein tyrosine kinase activator activity / regulation of dendritic spine morphogenesis / chemorepellent activity / negative regulation of cell adhesion / motor neuron axon guidance / retinal ganglion cell axon guidance / regulation of cell morphogenesis / EPH-Ephrin signaling / innervation / positive regulation of synapse assembly / adult walking behavior / regulation of GTPase activity / positive regulation of peptidyl-tyrosine phosphorylation / negative regulation of epithelial to mesenchymal transition / regulation of focal adhesion assembly / Somitogenesis / regulation of axonogenesis / positive regulation of amyloid-beta formation / EPHA-mediated growth cone collapse / regulation of cell-cell adhesion / positive regulation of intracellular signal transduction / negative regulation of long-term synaptic potentiation / basement membrane / cochlea development / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / axonal growth cone / ephrin receptor binding / axon terminus / cellular response to forskolin / positive regulation of cell adhesion / axon guidance / regulation of microtubule cytoskeleton organization / protein tyrosine kinase binding / peptidyl-tyrosine phosphorylation / negative regulation of cell migration / dendritic shaft / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / filopodium / adherens junction / neuromuscular junction / receptor protein-tyrosine kinase / postsynaptic density membrane / GABA-ergic synapse / caveola / negative regulation of ERK1 and ERK2 cascade / Schaffer collateral - CA1 synapse / cellular response to amyloid-beta / kinase activity / nervous system development / negative regulation of neuron projection development / amyloid-beta binding / protein autophosphorylation / presynaptic membrane / protein tyrosine kinase activity / early endosome membrane / perikaryon / dendritic spine / negative regulation of neuron apoptotic process / mitochondrial outer membrane / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein kinase activity / cell adhesion / negative regulation of translation / protein stabilization / positive regulation of cell migration / axon / external side of plasma membrane
Similarity search - Function
ephrin a2 ectodomain / Ephrin-A ectodomain / Ephrin type-A receptor 4, SAM domain / Ephrin type-A receptor 4, ligand binding domain / Ephrin receptor-binding domain / Ephrin, conserved site / Ephrin / Ephrin / Ephrin receptor-binding (ephrin RBD) domain signature. / Ephrin receptor-binding (ephrin RBD) domain profile. ...ephrin a2 ectodomain / Ephrin-A ectodomain / Ephrin type-A receptor 4, SAM domain / Ephrin type-A receptor 4, ligand binding domain / Ephrin receptor-binding domain / Ephrin, conserved site / Ephrin / Ephrin / Ephrin receptor-binding (ephrin RBD) domain signature. / Ephrin receptor-binding (ephrin RBD) domain profile. / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Tyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / : / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. / Receptor tyrosine kinase class V signature 2. / Eph receptor ligand-binding domain profile. / Ephrin receptor ligand binding domain / Putative ephrin-receptor like / SAM domain (Sterile alpha motif) / Galactose-binding domain-like / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Cupredoxins - blue copper proteins / Sterile alpha motif/pointed domain superfamily / Fibronectin type III domain / Cupredoxin / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Ribbon / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Jelly Rolls / Serine/Threonine protein kinases, catalytic domain / 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
Similarity search - Domain/homology
Ephrin-A5 / Ephrin type-A receptor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 Å
AuthorsXu, K. / Tsvetkova-Robev, D. / Xu, Y. / Goldgur, Y. / Chan, Y.-P. / Himanen, J.P. / Nikolov, D.B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Insights into Eph receptor tyrosine kinase activation from crystal structures of the EphA4 ectodomain and its complex with ephrin-A5.
Authors: Xu, K. / Tzvetkova-Robev, D. / Xu, Y. / Goldgur, Y. / Chan, Y.P. / Himanen, J.P. / Nikolov, D.B.
History
DepositionAug 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 2.2Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ephrin type-A receptor 4
B: Ephrin-A5
C: Ephrin type-A receptor 4
D: Ephrin-A5
E: Ephrin type-A receptor 4
F: Ephrin-A5
G: Ephrin type-A receptor 4
H: Ephrin-A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,85019
Polymers295,7918
Non-polymers4,05911
Water00
1
A: Ephrin type-A receptor 4
B: Ephrin-A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0185
Polymers73,9482
Non-polymers1,0703
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint5 kcal/mol
Surface area34690 Å2
MethodPISA
2
C: Ephrin type-A receptor 4
D: Ephrin-A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7974
Polymers73,9482
Non-polymers8492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-1 kcal/mol
Surface area34440 Å2
MethodPISA
3
E: Ephrin type-A receptor 4
F: Ephrin-A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0185
Polymers73,9482
Non-polymers1,0703
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint2 kcal/mol
Surface area34450 Å2
MethodPISA
4
G: Ephrin type-A receptor 4
H: Ephrin-A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0185
Polymers73,9482
Non-polymers1,0703
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint6 kcal/mol
Surface area35230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.541, 46.694, 262.305
Angle α, β, γ (deg.)90.00, 98.45, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23G
14B
24D
15B
25F
16B
26H
17C
27E
18C
28G
19D
29F
110D
210H
111E
211G
112F
212H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROASPASPAA27 - 5422 - 517
21PROPROASPASPCC27 - 5422 - 517
12PROPROASPASPAA27 - 5422 - 517
22PROPROASPASPEE27 - 5422 - 517
13PROPROASPASPAA27 - 5422 - 517
23PROPROASPASPGG27 - 5422 - 517
14ALAALACYSCYSBB26 - 1642 - 140
24ALAALACYSCYSDD26 - 1642 - 140
15VALVALCYSCYSBB28 - 1644 - 140
25VALVALCYSCYSFF28 - 1644 - 140
16VALVALCYSCYSBB28 - 1644 - 140
26VALVALCYSCYSHH28 - 1644 - 140
17PROPROASPASPCC27 - 5422 - 517
27PROPROASPASPEE27 - 5422 - 517
18PROPROASPASPCC27 - 5422 - 517
28PROPROASPASPGG27 - 5422 - 517
19VALVALCYSCYSDD28 - 1644 - 140
29VALVALCYSCYSFF28 - 1644 - 140
110VALVALCYSCYSDD28 - 1644 - 140
210VALVALCYSCYSHH28 - 1644 - 140
111PROPROASPASPEE27 - 5422 - 517
211PROPROASPASPGG27 - 5422 - 517
112VALVALMETMETFF28 - 1654 - 141
212VALVALMETMETHH28 - 1654 - 141

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

-
Components

#1: Protein
Ephrin type-A receptor 4 / EPH-like kinase 8 / EK8 / hEK8 / Tyrosine-protein kinase TYRO1 / Tyrosine-protein kinase receptor SEK


Mass: 57414.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA4, HEK8, SEK, TYRO1 / Organ (production host): ovary / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High5
References: UniProt: P54764, receptor protein-tyrosine kinase
#2: Protein
Ephrin-A5 / AL-1 / EPH-related receptor tyrosine kinase ligand 7 / LERK-7


Mass: 16533.562 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EFNA5, EPLG7, LERK7 / Organ (production host): ovary / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High5 / References: UniProt: P52803
#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.: 8
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: 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.: 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
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.25 Å3/Da / Density % sol: 71.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 2.0 M Sodium Acetate, 0.1 M Sodium Acetate buffer pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.13→30 Å / Num. all: 85812 / Num. obs: 84233 / % possible obs: 98.16 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 3.13→3.24 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 2 / % possible all: 96.4

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WO3

2wo3


Resolution: 3.13→30 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.881 / SU B: 52.412 / SU ML: 0.408 / Cross valid method: THROUGHOUT / ESU R: 3.377 / ESU R Free: 0.461 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. THE AUTHORS STATE THAT THE CONFORMATION ISSUE FOR NAG AS WELL AS THE HIGH REAL SPACE R-FACTORS ARE DUE TO THE PARTIAL DISORDER. THE DENSITY ...Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. THE AUTHORS STATE THAT THE CONFORMATION ISSUE FOR NAG AS WELL AS THE HIGH REAL SPACE R-FACTORS ARE DUE TO THE PARTIAL DISORDER. THE DENSITY IS OF POOR QUALITY AND THE MODEL PRIMARILY REFLECTS THAT THEY ARE THERE.
RfactorNum. reflection% reflectionSelection details
Rfree0.29044 4496 5 %RANDOM
Rwork0.24424 ---
obs0.24661 84233 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 148.921 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-2.31 Å2
2--5.36 Å20 Å2
3----6.09 Å2
Refinement stepCycle: LAST / Resolution: 3.13→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20681 0 266 0 20947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221520
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.681.9629300
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.41852613
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.19423.931028
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.411153416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.91715156
X-RAY DIFFRACTIONr_chiral_restr0.1050.23189
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02116622
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A6900.13
12C6900.13
21A6790.13
22E6790.13
31A6630.13
32G6630.13
41B1330.18
42D1330.18
51B1330.22
52F1330.22
61B1300.22
62H1300.22
71C6860.14
72E6860.14
81C6670.13
82G6670.13
91D1390.22
92F1390.22
101D1380.2
102H1380.2
111E6700.14
112G6700.14
121F1400.24
122H1400.24
LS refinement shellResolution: 3.13→3.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 302 -
Rwork0.331 5649 -
obs--99.72 %
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)
10.0652-0.0222-0.04850.1554-0.01510.93180.1031-0.06720.0738-0.2472-0.0285-0.22720.1524-0.3524-0.07460.8312-0.12980.46560.27170.00780.37625.317621.8663-85.8146
21.12720.24110.80060.12180.11080.67960.0850.2721-0.15790.11860.11660.069-0.06080.2835-0.20160.3381-0.00780.00490.4975-0.10310.494718.859622.4253-9.055
30.0633-0.0272-0.2160.02670.1021.18430.1026-0.01750.0597-0.05720.0250.0224-0.0002-0.2128-0.12760.6648-0.03040.01520.4505-0.07150.2364-96.8591-17.2009-85.32
41.09380.51340.32360.2910.1890.53170.03280.11210.01580.04790.04770.14760.1460.3103-0.08050.35950.03310.03120.4927-0.07290.4921-83.7113-15.1477-6.8742
50.0428-0.04540.04650.1148-0.15050.65840.1143-0.0533-0.1007-0.1180.00760.2025-0.01580.3192-0.12190.6495-0.0989-0.34490.34940.11390.4169-29.480334.1199-84.2786
61.05320.14730.03250.0649-0.03341.3695-0.0097-0.0725-0.1234-0.02440.14780.0612-0.1407-0.1722-0.13810.12520.0116-0.03970.58440.15420.5745-50.199210.5803-12.1355
70.09060.0030.13170.07060.03380.49910.0486-0.0695-0.0511-0.1342-0.08220.1166-0.07520.20190.03370.66360.1231-0.32330.5597-0.03420.2467-125.3165-8.5689-88.7871
81.2201-0.3246-0.31270.6344-0.73971.47070.09290.0830.0927-0.16210.00120.18070.242-0.1245-0.09410.09930.04020.00820.70970.0510.5326-152.2933-25.4187-17.1248
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 542
2X-RAY DIFFRACTION1A3401 - 3403
3X-RAY DIFFRACTION2B25 - 165
4X-RAY DIFFRACTION2B201 - 202
5X-RAY DIFFRACTION3C27 - 542
6X-RAY DIFFRACTION3C601 - 602
7X-RAY DIFFRACTION4D26 - 165
8X-RAY DIFFRACTION4D201 - 202
9X-RAY DIFFRACTION5E27 - 542
10X-RAY DIFFRACTION5E3401 - 3403
11X-RAY DIFFRACTION6F28 - 165
12X-RAY DIFFRACTION6F201 - 202
13X-RAY DIFFRACTION7G27 - 542
14X-RAY DIFFRACTION7G3401 - 3403
15X-RAY DIFFRACTION8H28 - 165
16X-RAY DIFFRACTION8H201 - 202

+
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