[English] 日本語
Yorodumi
- PDB-6wer: DENV2 NS1 in complex with neutralizing 2B7 Fab fragment -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wer
TitleDENV2 NS1 in complex with neutralizing 2B7 Fab fragment
Components
  • 2B7 Fab heavy chain
  • 2B7 Fab light chain
  • Non-structural protein 1
KeywordsVIRAL PROTEIN / Flavivirus NS1 / Antibody / Fab fragment
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / : / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / : / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A ...: / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesDengue virus 2
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.96 Å
AuthorsAkey, D.L. / Smith, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Science / Year: 2021
Title: Structural basis for antibody inhibition of flavivirus NS1-triggered endothelial dysfunction.
Authors: Biering, S.B. / Akey, D.L. / Wong, M.P. / Brown, W.C. / Lo, N.T.N. / Puerta-Guardo, H. / Tramontini Gomes de Sousa, F. / Wang, C. / Konwerski, J.R. / Espinosa, D.A. / Bockhaus, N.J. / ...Authors: Biering, S.B. / Akey, D.L. / Wong, M.P. / Brown, W.C. / Lo, N.T.N. / Puerta-Guardo, H. / Tramontini Gomes de Sousa, F. / Wang, C. / Konwerski, J.R. / Espinosa, D.A. / Bockhaus, N.J. / Glasner, D.R. / Li, J. / Blanc, S.F. / Juan, E.Y. / Elledge, S.J. / Mina, M.J. / Beatty, P.R. / Smith, J.L. / Harris, E.
History
DepositionApr 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Non-structural protein 1
B: Non-structural protein 1
C: 2B7 Fab heavy chain
D: 2B7 Fab light chain
E: 2B7 Fab heavy chain
F: 2B7 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,5028
Polymers195,0596
Non-polymers4422
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14550 Å2
ΔGint-78 kcal/mol
Surface area65750 Å2
Unit cell
Length a, b, c (Å)148.465, 148.465, 517.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPASNASN(chain 'A' and (resid 1 through 82 or resid 84...AA1 - 8225 - 106
121VALVALPROPRO(chain 'A' and (resid 1 through 82 or resid 84...AA84 - 106108 - 130
131ASNASNTYRTYR(chain 'A' and (resid 1 through 82 or resid 84...AA130 - 158154 - 182
141THRTHRLYSLYS(chain 'A' and (resid 1 through 82 or resid 84...AA164 - 172188 - 196
151LYSLYSLYSLYS(chain 'A' and (resid 1 through 82 or resid 84...AA174198
161ASPASPASNASN(chain 'A' and (resid 1 through 82 or resid 84...AA176 - 255200 - 279
171ARGARGTHRTHR(chain 'A' and (resid 1 through 82 or resid 84...AA257 - 288281 - 312
181ASPASPLEULEU(chain 'A' and (resid 1 through 82 or resid 84...AA290 - 349314 - 373
291ASPASPASNASN(chain 'B' and (resid 1 through 82 or resid 84...BB1 - 8225 - 106
2101VALVALPROPRO(chain 'B' and (resid 1 through 82 or resid 84...BB84 - 106108 - 130
2111ASNASNTYRTYR(chain 'B' and (resid 1 through 82 or resid 84...BB130 - 158154 - 182
2121THRTHRLYSLYS(chain 'B' and (resid 1 through 82 or resid 84...BB164 - 172188 - 196
2131LYSLYSLYSLYS(chain 'B' and (resid 1 through 82 or resid 84...BB174198
2141ASPASPASNASN(chain 'B' and (resid 1 through 82 or resid 84...BB176 - 255200 - 279
2151ARGARGTHRTHR(chain 'B' and (resid 1 through 82 or resid 84...BB257 - 288281 - 312
2161ASPASPLEULEU(chain 'B' and (resid 1 through 82 or resid 84...BB290 - 349314 - 373
1172GLUGLUPROPROchain 'C'CC1 - 13220 - 152
1182GLYGLYSERSERchain 'C'CC135 - 162155 - 182
1192SERSERSERSERchain 'C'CC167 - 219187 - 239
2202GLUGLUPROPROchain 'E'EE1 - 13220 - 152
2212GLYGLYSERSERchain 'E'EE135 - 162155 - 182
2222SERSERSERSERchain 'E'EE167 - 219187 - 239
1233ASNASNARGARGchain 'D'DD1 - 21521 - 235
2243ASNASNARGARGchain 'F'FF1 - 21521 - 235

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein Non-structural protein 1


Mass: 42674.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 2 / Production host: unidentified baculovirus / References: UniProt: D0EPS0, UniProt: P29990*PLUS
#2: Antibody 2B7 Fab heavy chain


Mass: 28651.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody 2B7 Fab light chain


Mass: 26204.037 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#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 / N-Acetylglucosamine


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
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 66.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 23% PEG 3350, 0.25 M MgCl2, 0.1 M sodium acetate pH 5.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.96→29.8 Å / Num. obs: 25742 / % possible obs: 98.81 % / Redundancy: 26.6 % / Biso Wilson estimate: 194.67 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.2152 / Rpim(I) all: 0.04245 / Rrim(I) all: 0.2194 / Net I/σ(I): 13.77
Reflection shellResolution: 3.96→4.01 Å / Redundancy: 24.5 % / Rmerge(I) obs: 4.703 / Mean I/σ(I) obs: 0.92 / Num. unique obs: 2415 / CC1/2: 0.703 / CC star: 0.909 / Rpim(I) all: 0.9601 / Rrim(I) all: 4.803 / % possible all: 95.34

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
JBluIce-EPICSdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4o6b
Resolution: 3.96→29.8 Å / SU ML: 0.7552 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.2483
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3113 1276 5 %
Rwork0.2756 24266 -
obs0.2773 25542 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 252.64 Å2
Refinement stepCycle: LAST / Resolution: 3.96→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11710 0 0 0 11710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002911987
X-RAY DIFFRACTIONf_angle_d0.658116286
X-RAY DIFFRACTIONf_chiral_restr0.04381816
X-RAY DIFFRACTIONf_plane_restr0.00452074
X-RAY DIFFRACTIONf_dihedral_angle_d20.91834351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.96-4.110.47271320.43592547X-RAY DIFFRACTION95.13
4.12-4.30.39351400.38282639X-RAY DIFFRACTION99.11
4.3-4.530.33631410.33952648X-RAY DIFFRACTION99.36
4.53-4.810.33451400.32632676X-RAY DIFFRACTION99.29
4.81-5.180.33771400.31992660X-RAY DIFFRACTION99.29
5.18-5.70.33951430.31262712X-RAY DIFFRACTION99.76
5.7-6.510.2961420.31032719X-RAY DIFFRACTION99.76
6.52-8.180.30641460.26992761X-RAY DIFFRACTION100
8.18-29.80.27891520.21582904X-RAY DIFFRACTION99.87
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.888764303441.8791205911-0.89822618810.64153098108-0.1255110694176.20226431274-0.3710918155320.05604943212890.8463328280190.948596557462-0.955083909672-0.466471625314-4.14120340433.72406739044-0.06895173427372.339335580050.06159036376920.02486541823054.412159436810.2147526062412.905552467124.8912260105837.1128447389-52.2349174789
23.196162839270.489320903467-5.048014485822.58592502267-1.470143328891.832241476030.243008129775-0.287655528338-0.04033170288210.2799482448650.09713098144660.02259068299080.415144584071-1.440994243290.0002541989441342.74745691557-0.143618841670.05915888884962.798286312430.08171717970452.1471900044812.58759166237.47843017816-36.7753747964
3-0.7246695317210.7364230731130.5672242169241.845265074480.303628696166-0.301608858470.74927676359-2.58949354905-2.50617686249-0.9823243006851.19875073851-2.50130145755-2.887337265581.345861658650.007536956171952.311099883080.2109041393040.05154931464492.397891354270.1840192812352.2538472767318.65437678236.3944548396-29.7391167751
42.789908619713.47110759793-1.951238311283.15214663438-2.418266749481.25691484172.066562887153.677258134361.069289897320.507749794877-1.317265168890.1974960537783.894947381840.09718268836840.01126201969143.46631350515-0.1141837279230.1147875301713.43476018749-0.1876962984572.1553863694313.398186017512.8265427764-45.0370264258
51.568473176731.622757760450.2655154342264.39648675281.140918978686.98376395469-0.2885785417450.3055867168760.5353774267580.0149771659450.424780628896-0.0490886055264-0.3555354911250.0443882630070.0007045027391342.32779026093-0.01481397070520.2177420500742.9968991381-0.004770343223062.3519373985625.071207565136.3388247532-37.73942209
63.16848756515-1.876987692691.464161608951.39989877794-0.3665868507370.840119952869-0.2569647078230.843396026526-0.88365314551-0.9971580250081.325234227312.852180348113.95860894744-1.106509454130.001414834679732.42396330657-0.2339018848870.3026208969784.700702823020.4438368361673.96983244784.4199832926734.6702646285-62.4145463096
70.04058740272-3.50487114018-0.6986093939751.953117190281.717233679952.935328509490.0398027340522-0.5432022608610.8837142791441.735954420811.28580876280.95042155444-2.87103892536-1.17089741163-0.001507528840233.307034177-0.007360338090040.07542375451192.823548750160.07943870068342.8110008868621.795234429959.9527893498-76.2201014956
81.156078820881.98817652814-0.5063604926640.264816171463-0.5948248111654.159208768710.1705888753310.735001860696-0.0524267441532-0.244751592733-0.0935145932609-0.100940394407-0.701373389902-0.102505626328-0.000484440821122.72846147804-0.07612473411360.07988921221133.409783502930.2329139274232.2452676627727.88230791156.465060619-82.5126577531
91.703289066340.999796107618-0.2920229079445.46011175609-0.9624449410215.66615349968-0.01565127234640.2454167802140.08924581266690.4735879499430.258142895967-0.06437125663150.22690245446-0.711113284130.0003896383256592.010182167540.1495993592290.02464184136693.688133327380.1851580296222.3829166677423.029432812830.4690583189-75.3720113333
106.62850785223-4.71785232516-4.023643746443.368507493591.517722624633.361803337440.219588249260.8148045585780.05826718405840.0656312317645-0.1757067154190.195482926971-0.208109822991-1.15685427357-0.0002493715215452.762860683410.3077556072870.124134784072.549111673210.1729861721512.50783632373-3.0964058618740.41090552-15.2087343824
115.950611061154.0507716839-0.7235569689365.77739556777.497010166855.46963303674-1.201558668320.1300264246141.30897875464-0.5222082270060.0634706638080.413604955006-1.628960054420.5472153114320.0008700848269752.366780561680.125678122266-0.07890718756412.09684719003-0.01236326202032.58439108851-17.247109281144.956992893213.6864954302
12-0.625888031858-1.413298531761.279231506054.669139600552.786109867.7355762944-0.217604337641-0.469179655199-0.710518105652-0.33729944889-0.00367077258954-0.7576341724890.01394477875091.612182067930.0006621676900482.623738776940.4381876428320.1744926139652.48970892134-0.1053270708282.3899243361111.056951671429.2834601127-0.802848490968
135.76334182602-7.027631051872.164473481132.169489725420.334239044926.742425267030.199721060565-0.629465273634-0.752995307805-0.2170188771410.08840982283850.677376394293-0.537014431263-0.351112591155-3.93468104803E-52.98428289381-0.1102698735690.5702053901562.80016187524-0.05782613031173.00005206622-20.02993616730.992602339520.4483741011
147.304044423681.81961291637-0.39639428280.378002190249-3.581227867112.649494724591.00670919006-0.02190277603510.7955608359290.563171389243-0.5022075130291.06463654217-0.05117526790280.05681569670950.0004213030688782.10905862566-0.12663390350.1663782230852.515188594670.4870349952833.18005432706-2.36473172532.4179171949-101.213303485
153.39007434654-6.84522879508-3.051586765513.418033445524.95561395832.110562249580.1213769316010.6722453648750.887978228977-0.2798419190860.188379525939-0.02234675422880.8187128739431.677426303180.0005770340480222.87496065172-0.831629413242-0.07414395290432.684528198530.2581090008893.1502471661-13.184829777629.195086819-131.524571122
164.66778914045-2.23008417104-2.618955821031.5666930956-1.93777045348.166051525657.91192880795E-50.3823084966880.808652426295-0.111309136766-0.430016743147-0.297544843089-0.4990307259831.2910398936-0.0004439334280762.52066155202-0.529372131653-0.0755784151852.742572393650.01806529508732.4629470509815.810260024637.9700822098-114.385204817
170.33210280031.622997548161.05910640144-0.6009174949054.274325813376.00395483672-2.24099756386-0.3223127013011.50293437552-0.9194530146490.3951003521870.934919720263-1.766451465311.661594996389.94802336067E-52.8911907489-0.30808567765-0.7081355108782.78160793994-0.01796396504063.37549136413-12.01755391542.867686699-139.292895591
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 105 )
3X-RAY DIFFRACTION3chain 'A' and (resid 106 through 144 )
4X-RAY DIFFRACTION4chain 'A' and (resid 145 through 171 )
5X-RAY DIFFRACTION5chain 'A' and (resid 172 through 349 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 32 )
7X-RAY DIFFRACTION7chain 'B' and (resid 33 through 81 )
8X-RAY DIFFRACTION8chain 'B' and (resid 82 through 144 )
9X-RAY DIFFRACTION9chain 'B' and (resid 145 through 349 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 125 )
11X-RAY DIFFRACTION11chain 'C' and (resid 126 through 219 )
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 117 )
13X-RAY DIFFRACTION13chain 'D' and (resid 118 through 215 )
14X-RAY DIFFRACTION14chain 'E' and (resid 1 through 125 )
15X-RAY DIFFRACTION15chain 'E' and (resid 126 through 219 )
16X-RAY DIFFRACTION16chain 'F' and (resid 1 through 117 )
17X-RAY DIFFRACTION17chain 'F' and (resid 118 through 215 )

+
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