[English] 日本語
Yorodumi
- PDB-7ceb: Crystal structure of alpha6beta1 integrin headpiece -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ceb
TitleCrystal structure of alpha6beta1 integrin headpiece
Components
  • Integrin alpha-6
  • Integrin beta-1
  • TS2/16 VH(S112C)-SARAH
  • TS2/16 VL-SARAH(S37C)
KeywordsCELL ADHESION/IMMUNE SYSTEM / Integrin / Fv-clasp / Laminin / CELL ADHESION / CELL ADHESION-IMMUNE SYSTEM complex
Function / homology
Function and homology information


ectodermal cell differentiation / integrin alpha8-beta1 complex / neuregulin binding / Type I hemidesmosome assembly / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha6-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex ...ectodermal cell differentiation / integrin alpha8-beta1 complex / neuregulin binding / Type I hemidesmosome assembly / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha6-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex / positive regulation of glutamate uptake involved in transmission of nerve impulse / myoblast fate specification / integrin alpha9-beta1 complex / regulation of collagen catabolic process / cardiac cell fate specification / integrin alpha1-beta1 complex / integrin binding involved in cell-matrix adhesion / nail development / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / reactive gliosis / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / formation of radial glial scaffolds / Other semaphorin interactions / cerebellar climbing fiber to Purkinje cell synapse / Formation of the ureteric bud / myelin sheath abaxonal region / CD40 signaling pathway / calcium-independent cell-matrix adhesion / Fibronectin matrix formation / positive regulation of fibroblast growth factor receptor signaling pathway / regulation of synapse pruning / integrin alphav-beta1 complex / skin morphogenesis / CHL1 interactions / basement membrane organization / cardiac muscle cell myoblast differentiation / MET interacts with TNS proteins / Laminin interactions / cardiac muscle cell differentiation / Platelet Adhesion to exposed collagen / germ cell migration / leukocyte tethering or rolling / insulin-like growth factor I binding / cell projection organization / myoblast fusion / positive regulation of vascular endothelial growth factor signaling pathway / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / myoblast differentiation / axon extension / cell migration involved in sprouting angiogenesis / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / central nervous system neuron differentiation / regulation of spontaneous synaptic transmission / wound healing, spreading of epidermal cells / positive regulation of fibroblast migration / integrin complex / lamellipodium assembly / Assembly of collagen fibrils and other multimeric structures / sarcomere organization / heterotypic cell-cell adhesion / MET activates PTK2 signaling / Molecules associated with elastic fibres / Basigin interactions / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / negative regulation of vasoconstriction / leukocyte migration / leukocyte cell-cell adhesion / muscle organ development / cell adhesion mediated by integrin / Syndecan interactions / positive regulation of wound healing / dendrite morphogenesis / negative regulation of neuron differentiation / positive regulation of neuroblast proliferation / negative regulation of Rho protein signal transduction / response to muscle activity / maintenance of blood-brain barrier / cell-substrate adhesion / homophilic cell-cell adhesion / TGF-beta receptor signaling activates SMADs / cleavage furrow / establishment of mitotic spindle orientation / fibronectin binding / negative regulation of anoikis / intercalated disc / cellular response to low-density lipoprotein particle stimulus / positive regulation of GTPase activity / RHOG GTPase cycle / glial cell projection / neuroblast proliferation / RAC2 GTPase cycle / RAC3 GTPase cycle / ECM proteoglycans / phagocytosis / Integrin cell surface interactions
Similarity search - Function
Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta tail domain / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin EGF domain / Integrin beta subunit, tail ...Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta tail domain / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain, extracellular / EGF-like domain / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1.
Similarity search - Domain/homology
Integrin beta-1 / Integrin alpha-6
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsArimori, T. / Takagi, J.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H02389 Japan
Japan Agency for Medical Research and Development (AMED)19am0101075 Japan
CitationJournal: Nat Commun / Year: 2021
Title: Structural mechanism of laminin recognition by integrin.
Authors: Takao Arimori / Naoyuki Miyazaki / Emiko Mihara / Mamoru Takizawa / Yukimasa Taniguchi / Carlos Cabañas / Kiyotoshi Sekiguchi / Junichi Takagi /
Abstract: Recognition of laminin by integrin receptors is central to the epithelial cell adhesion to basement membrane, but the structural background of this molecular interaction remained elusive. Here, we ...Recognition of laminin by integrin receptors is central to the epithelial cell adhesion to basement membrane, but the structural background of this molecular interaction remained elusive. Here, we report the structures of the prototypic laminin receptor α6β1 integrin alone and in complex with three-chain laminin-511 fragment determined via crystallography and cryo-electron microscopy, respectively. The laminin-integrin interface is made up of several binding sites located on all five subunits, with the laminin γ1 chain C-terminal portion providing focal interaction using two carboxylate anchor points to bridge metal-ion dependent adhesion site of integrin β1 subunit and Asn189 of integrin α6 subunit. Laminin α5 chain also contributes to the affinity and specificity by making electrostatic interactions with large surface on the β-propeller domain of α6, part of which comprises an alternatively spliced X1 region. The propeller sheet corresponding to this region shows unusually high mobility, suggesting its unique role in ligand capture.
History
DepositionJun 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integrin alpha-6
B: Integrin beta-1
C: TS2/16 VH(S112C)-SARAH
D: TS2/16 VL-SARAH(S37C)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,53415
Polymers158,0224
Non-polymers1,51211
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10520 Å2
ΔGint-48 kcal/mol
Surface area51810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.520, 251.310, 63.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Integrin alpha-6 / CD49 antigen-like family member F / VLA-6


Mass: 69776.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA6 / Production host: Homo sapiens (human) / References: UniProt: P23229
#2: Protein Integrin beta-1 / Fibronectin receptor subunit beta / Glycoprotein IIa / GPIIA / VLA-4 subunit beta


Mass: 50510.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB1, FNRB, MDF2, MSK12 / Production host: Homo sapiens (human) / References: UniProt: P05556

-
Antibody , 2 types, 2 molecules CD

#3: Antibody TS2/16 VH(S112C)-SARAH


Mass: 19463.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: chimera of TS2/16 VH(S112C)-SARAH
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli (E. coli)
#4: Antibody TS2/16 VL-SARAH(S37C)


Mass: 18270.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: chimera of TS2/16 VL-SARAH(S37C)
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli (E. coli)

-
Sugars , 1 types, 6 molecules

#6: 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.: 6
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

-
Non-polymers , 3 types, 8 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 23% PEG1000, 0.2 M NaCl, 0.1 M Na/K phosphate, pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.89→47.8 Å / Num. obs: 42251 / % possible obs: 99.6 % / Redundancy: 9.75 % / Biso Wilson estimate: 72.74 Å2 / CC1/2: 0.997 / Rsym value: 0.158 / Net I/σ(I): 12.48
Reflection shellResolution: 2.89→3.07 Å / Mean I/σ(I) obs: 1.63 / Num. unique obs: 6580 / CC1/2: 0.806

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wk0, 3vi3, 5xcx

4wk0

3vi3

5xcx


Resolution: 2.89→44.57 Å / SU ML: 0.402 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3919 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2486 2038 4.83 %
Rwork0.2066 40180 -
obs0.2088 42218 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.68 Å2
Refinement stepCycle: LAST / Resolution: 2.89→44.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9540 0 89 3 9632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00399831
X-RAY DIFFRACTIONf_angle_d0.773713307
X-RAY DIFFRACTIONf_chiral_restr0.05461471
X-RAY DIFFRACTIONf_plane_restr0.00481724
X-RAY DIFFRACTIONf_dihedral_angle_d11.76925901
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.960.39011250.33072481X-RAY DIFFRACTION94.01
2.96-3.040.36371340.3062653X-RAY DIFFRACTION99.86
3.04-3.120.32561340.27232625X-RAY DIFFRACTION99.86
3.12-3.210.32991440.26532635X-RAY DIFFRACTION99.93
3.21-3.310.30451250.27022713X-RAY DIFFRACTION100
3.31-3.430.32711370.23812615X-RAY DIFFRACTION99.96
3.43-3.570.27451230.22082674X-RAY DIFFRACTION100
3.57-3.730.22981310.2052686X-RAY DIFFRACTION100
3.73-3.930.25511290.20332678X-RAY DIFFRACTION100
3.93-4.170.23131360.18322676X-RAY DIFFRACTION100
4.17-4.50.20941520.15962681X-RAY DIFFRACTION100
4.5-4.950.1971270.14992709X-RAY DIFFRACTION100
4.95-5.660.17061440.16192710X-RAY DIFFRACTION100
5.66-7.130.25551540.20962757X-RAY DIFFRACTION100
7.13-44.570.25991430.23032887X-RAY DIFFRACTION99.47
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)
10.1538432990240.01215995082090.0899633945125-0.006275971671540.01825966607030.06340099919530.001965017172340.159715347486-0.017657262010.4402821802950.140674545863-0.3682927242360.1709096558910.0961042496292-0.001588818170320.589912361690.0543762999294-0.03295619021120.5885926162680.03253220739951.1408798685195.06472631246.709515956240.0774455772023
20.8796542787180.0681698541907-0.3948374484711.115499685770.4537047227911.10411898859-0.0555465738072-0.0733367172109-0.288395571318-0.0485946888466-0.02826422498490.2298252865860.0751396417793-0.0804891009625-0.05564387275530.3871438661390.00398024313874-0.04271303614130.409966821650.06742838385750.45351496502921.059832107833.821968009312.7634295879
30.0464547601295-0.113117050469-0.1170641719110.301738850328-0.2471867338550.3958567450660.297959180172-0.448648576986-0.108153084480.06071316225450.183780658918-0.2586146768660.0347383850114-0.08634400582620.02256737114880.3796080319510.04424336473250.3245269168270.66533883978-0.266923183420.22100409462223.825783634972.678728871239.4366963094
40.135774476556-0.005783067910240.101746622230.00312069619573-0.00209638868260.02001946430850.07994196259290.0359901656749-0.27324129033-0.364760909431-0.0594185770107-0.0500277233962-0.1774477547930.1630284817010.01821582898490.8955665680630.06572063531760.1113127141770.849071412481-0.1586475708870.46102168853224.021367208566.476713197635.3470709578
51.066273506110.01732818468870.397673620140.279543841746-0.4363030341622.569399887330.360248303888-0.554793788945-0.00367435133570.235287753505-0.4172645547130.5550004011910.340446932330.332199614216-0.02206951280340.641218282063-0.1889672096830.1524117528970.762484659629-0.08700596864780.97266406670965.744575595864.3496151213-0.446453740188
61.94122822874-0.0738645014209-0.781638742962.44776502677-0.3352671088620.766820640489-0.08337779065450.236431299194-0.0916681284807-0.4168011685410.0982437859310.12224062530.0654369009730.05912468728850.0125988503240.5567243656450.0288114912851-0.01953162861830.5159905882950.03327536815240.3469308991651.429253711235.3154792382-10.3980683193
72.0079071616-0.54558144669-0.9840019095391.2707128980.591806735750.854737449905-0.005620508702630.00691522756945-0.0809407318685-0.1615388127720.01485864733540.0268883255833-0.03016942272510.00441556361950.002263581550170.453404819624-0.0122377258386-0.05156540058510.411486808470.003594438994350.41275012942547.037606363132.7275482977-7.57530066647
81.39892471663-0.268179668547-0.3600146534942.314120554240.5490056797912.546371512930.224055823834-0.3197584315750.5038632112470.546771165495-0.1599689963480.7599435681880.0698678260911-0.300495644591-0.1573761989550.6266753977-0.1485845786060.2016663629180.601798501211-0.04738461960810.81219185327853.561055410560.268322894-1.61053057037
90.0553878306037-0.05824011645860.07240422013190.0768809978013-0.02934674263150.0575863690590.08666553266690.120761195906-0.393436729142-0.0799983443287-0.0801028996114-0.0991506545680.216220230770.0178920500648-0.0003443482021610.575061836923-0.005929461630990.03831052652730.586015407574-0.1562550532970.59954804788778.79057507948.24776405082-15.9514291977
100.07707805524590.0374409295877-0.02907765954350.0845763472166-0.0755051844880.08167404388990.1709733011880.136064627931-0.0290646732962-0.0902128030861-0.281628852883-0.241212988499-0.09920766257280.1523683255030.000785716226250.542015543296-0.06200894856090.1144420947110.755672653568-0.06636877671220.72610323884776.983623068119.5976354875-16.6390392073
110.065728485448-0.02377400191480.01014436913730.01703196358950.01432948295910.1720173800250.2176960825820.2015300260410.167563736353-0.204046142771-0.2388378106740.0200009579558-0.002861153753360.101881325648-0.001648148682670.8196871198040.06237628210190.1951848074790.888507108393-0.1134202575930.73505170870880.192471612812.8603212014-22.5515631493
120.04960869241460.0168227457359-0.00487551607230.0283210761488-0.01403130582810.0255670258581-0.03809240304620.201816548821-0.04360143467350.1127294321760.0195106578407-0.1188511874830.0963311672679-0.31501237309-0.0004905747465850.5253772559820.0204334897489-0.07882828027560.521695692668-0.1322250652590.59647420782273.524691351112.8446581045-9.11956413074
130.007733437029540.01606524343270.0479926229665-0.0233273116086-0.05513754133970.03535184616340.2635531671150.0188707264648-0.01750822081580.04100229815830.0582109198963-0.4084787378210.1438871027830.4122490175650.000243257294420.739881837430.0555701627353-0.1804544354360.860692407615-0.03385811237271.23057292086101.1417751696.460090191323.0975223242
14-0.0165352639791-0.004299755941990.009736087856360.01990603255430.0192459382680.0128953284934-0.1691651626210.08548993508520.1628991755060.1093656315220.0617489470686-0.281324783318-0.07851114009590.04459885612750.0003331011960170.604296869923-0.0114735242266-0.02816180287590.53036634196-0.146887131770.7042238976482.368936832125.67903279496.10533492951
150.163536352009-0.00550138693391-0.03038504969840.1012752977480.09795053944310.09901328324180.00498656667947-0.1457443605020.0992675682581-0.07301999159750.111899473495-0.199180541153-0.0551905237746-0.0938085488843-0.000109498777180.325350647979-0.00544664661911-0.08569812775790.392617321286-0.07030236203270.42803871395976.99308045919.30452433094.7746886717
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 120 through 149 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1 through 425 )
3X-RAY DIFFRACTION3chain 'A' and (resid 426 through 562 )
4X-RAY DIFFRACTION4chain 'A' and (resid 563 through 599 )
5X-RAY DIFFRACTION5chain 'B' and (resid 61 through 89 )
6X-RAY DIFFRACTION6chain 'B' and (resid 90 through 198 )
7X-RAY DIFFRACTION7chain 'B' and (resid 199 through 359 )
8X-RAY DIFFRACTION8chain 'B' and (resid 360 through 442 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 40 )
10X-RAY DIFFRACTION10chain 'C' and (resid 41 through 63 )
11X-RAY DIFFRACTION11chain 'C' and (resid 64 through 87 )
12X-RAY DIFFRACTION12chain 'C' and (resid 88 through 106 )
13X-RAY DIFFRACTION13chain 'C' and (resid 107 through 163 )
14X-RAY DIFFRACTION14chain 'D' and (resid 1 through 18 )
15X-RAY DIFFRACTION15chain 'D' and (resid 19 through 119 )

+
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