[English] 日本語
Yorodumi
- PDB-6d8w: Crystal structure of InvbI.18715.a.KN11: Influenza hemagglutinin ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6d8w
TitleCrystal structure of InvbI.18715.a.KN11: Influenza hemagglutinin from strain A/Jiangsu/ALSI/2011
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / Inflenza hemagglutinin / Structural Genomics / STRIVE / SSGCID / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane
Similarity search - Function
Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / OXAMIC ACID / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Sci Rep / Year: 2023
Title: Structural characterisation of hemagglutinin from seven Influenza A H1N1 strains reveal diversity in the C05 antibody recognition site.
Authors: Ghafoori, S.M. / Petersen, G.F. / Conrady, D.G. / Calhoun, B.M. / Stigliano, M.Z.Z. / Baydo, R.O. / Grice, R. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E. / Forwood, J.K.
History
DepositionApr 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2May 24, 2023Group: Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,10920
Polymers336,2446
Non-polymers1,86414
Water16,376909
1
A: Hemagglutinin
D: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,23111
Polymers168,1223
Non-polymers1,1098
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10730 Å2
ΔGint-31 kcal/mol
Surface area57150 Å2
MethodPISA
2
B: Hemagglutinin
C: Hemagglutinin
E: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,8789
Polymers168,1223
Non-polymers7566
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10940 Å2
ΔGint-42 kcal/mol
Surface area57900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.300, 113.330, 130.120
Angle α, β, γ (deg.)110.160, 90.850, 90.280
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 7 and (name N or name...
21(chain B and ((resid 7 and (name N or name...
31(chain C and ((resid 7 and (name N or name...
41(chain D and (resid 7 through 12 or (resid 13...
51(chain E and ((resid 7 and (name N or name...
61(chain F and ((resid 7 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 7 and (name N or name...A7
121(chain A and ((resid 7 and (name N or name...A4 - 600
131(chain A and ((resid 7 and (name N or name...A4 - 600
141(chain A and ((resid 7 and (name N or name...A4 - 600
151(chain A and ((resid 7 and (name N or name...A4 - 600
211(chain B and ((resid 7 and (name N or name...B7
221(chain B and ((resid 7 and (name N or name...B1 - 600
231(chain B and ((resid 7 and (name N or name...B1 - 600
241(chain B and ((resid 7 and (name N or name...B1 - 600
251(chain B and ((resid 7 and (name N or name...B1 - 600
311(chain C and ((resid 7 and (name N or name...C7
321(chain C and ((resid 7 and (name N or name...C2 - 486
331(chain C and ((resid 7 and (name N or name...C2 - 486
341(chain C and ((resid 7 and (name N or name...C2 - 486
351(chain C and ((resid 7 and (name N or name...C2 - 486
411(chain D and (resid 7 through 12 or (resid 13...D7 - 12
421(chain D and (resid 7 through 12 or (resid 13...D13 - 15
431(chain D and (resid 7 through 12 or (resid 13...D7 - 486
441(chain D and (resid 7 through 12 or (resid 13...D7 - 486
451(chain D and (resid 7 through 12 or (resid 13...D7 - 486
461(chain D and (resid 7 through 12 or (resid 13...D7 - 486
511(chain E and ((resid 7 and (name N or name...E7
521(chain E and ((resid 7 and (name N or name...E3 - 491
531(chain E and ((resid 7 and (name N or name...E3 - 491
541(chain E and ((resid 7 and (name N or name...E3 - 491
551(chain E and ((resid 7 and (name N or name...E3 - 491
611(chain F and ((resid 7 and (name N or name...F7
621(chain F and ((resid 7 and (name N or name...F3 - 601
631(chain F and ((resid 7 and (name N or name...F3 - 601
641(chain F and ((resid 7 and (name N or name...F3 - 601
651(chain F and ((resid 7 and (name N or name...F3 - 601

-
Components

#1: Protein
Hemagglutinin /


Mass: 56040.707 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G0Z9B7
#2: 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.: 5 / Source method: obtained synthetically / 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
#3: Chemical
ChemComp-OXM / OXAMIC ACID / Oxamic acid


Mass: 89.050 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3NO3
#4: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 909 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: SEC purified InvbI.18715.a.KN11.PD38282 at 10.18mg/ml (in 25mM MES pH 6.5, 150mM NaCl) was crystallized by sitting drop vapor diffusion at 14C with an equal volume (0.2:0.2uL) of protein: ...Details: SEC purified InvbI.18715.a.KN11.PD38282 at 10.18mg/ml (in 25mM MES pH 6.5, 150mM NaCl) was crystallized by sitting drop vapor diffusion at 14C with an equal volume (0.2:0.2uL) of protein:mother liquor (20mM each sodium formate, ammonium acetate, sodium citrate, sodium potassium tartrate, and sodium oxamate, 0.1M HEPES pH6.8, 17.2% PEG 500 MME, 8.6% PEG20k), then directly frozen for data collection. Crystal ID 297353a3 data set sht6-6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.35→43.292 Å / Num. obs: 146567 / % possible obs: 97.4 % / Redundancy: 2.641 % / Biso Wilson estimate: 40.16 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.079 / Χ2: 1.024 / Net I/σ(I): 11.91 / Num. measured all: 387137 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.35-2.412.6610.5492.13108580.7410.69196.9
2.41-2.482.6640.4582.6104510.8170.57597
2.48-2.552.660.42.96102570.8570.50297.1
2.55-2.632.6650.3413.4999280.8930.42897
2.63-2.712.660.2674.3596630.9360.33697.2
2.71-2.812.6620.2035.6394190.9620.25497.4
2.81-2.912.6580.1597.0589850.9720.297.2
2.91-3.032.6540.1258.6386350.980.15797.3
3.03-3.172.6410.09111.2183240.9890.11497.5
3.17-3.322.6410.07413.5780130.9920.09397.5
3.32-3.52.630.05616.4275920.9940.07197.6
3.5-3.722.620.04719.0771760.9950.0697.8
3.72-3.972.6190.0421.1767580.9960.05197.9
3.97-4.292.6150.03523.6663080.9970.04598.1
4.29-4.72.6080.03225.6858120.9970.0498.1
4.7-5.252.610.03225.8352630.9980.0498.2
5.25-6.072.6110.03325.3346320.9970.04298.2
6.07-7.432.60.03225.7539090.9970.04198.2
7.43-10.512.5940.02629.5530010.9980.03397.7
10.51-43.2922.5630.02631.115830.9970.03393.8

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vli,2wr0

5vli

2wr0


Resolution: 2.35→43.292 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 25.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2247 2041 1.39 %
Rwork0.1792 144475 -
obs0.1798 146516 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164.11 Å2 / Biso mean: 60.4921 Å2 / Biso min: 16.76 Å2
Refinement stepCycle: final / Resolution: 2.35→43.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21388 0 121 916 22425
Biso mean--86.5 48.47 -
Num. residues----2829
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A10879X-RAY DIFFRACTION10.89TORSIONAL
12B10879X-RAY DIFFRACTION10.89TORSIONAL
13C10879X-RAY DIFFRACTION10.89TORSIONAL
14D10879X-RAY DIFFRACTION10.89TORSIONAL
15E10879X-RAY DIFFRACTION10.89TORSIONAL
16F10879X-RAY DIFFRACTION10.89TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.40460.30991370.25589613975097
2.4046-2.46480.32831300.23189527965797
2.4648-2.53140.28371170.23129610972797
2.5314-2.60590.29431410.22329608974997
2.6059-2.690.28991330.22419677981097
2.69-2.78610.29491250.21079586971197
2.7861-2.89760.23841450.219579972497
2.8976-3.02950.30061320.20869622975497
3.0295-3.18910.24141380.1989639977798
3.1891-3.38890.22131660.19079632979898
3.3889-3.65040.221440.17379636978098
3.6504-4.01750.19981220.15599701982398
4.0175-4.59830.17441420.1389676981898
4.5983-5.79120.18611340.14489709984398
5.7912-43.29950.19941350.17429660979597
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)
10.6381-0.0352-0.18750.03030.06644.86210.00480.3391-0.0039-0.3967-0.15230.2535-0.3746-0.53020.12520.57140.0542-0.11460.46460.04610.3940.9244-51.2472-59.3394
21.70090.1781-0.27283.13440.78892.312-0.0061-0.0977-0.12360.28050.09490.14440.2589-0.2074-0.09590.2134-0.03940.01290.22120.0550.29746.9327-59.3923-24.6597
30.47820.3565-0.00230.2660.59041.07030.06830.3824-0.0108-0.36870.03320.1782-0.1341-0.4859-0.14530.80590.0397-0.14680.72090.04310.37723.1741-54.5736-78.1657
40.66630.48870.92450.61450.08362.0143-0.03650.4277-0.1246-0.65180.2920.1535-0.2548-0.2547-0.13070.91070.0331-0.18170.8621-0.05150.35498.6884-57.0726-94.9511
51.06910.21170.51880.27960.04573.1149-0.17010.32710.2672-0.1276-0.0640.2263-0.4038-0.32760.20410.33140.0656-0.03370.36680.05840.4035-34.51854.4223-57.6972
62.72090.15981.17581.3997-0.29032.29820.0857-0.48530.14650.1795-0.0483-0.0171-0.0884-0.2815-0.04750.17380.00080.06210.2662-0.03920.2798-26.4254-4.2895-27.0352
71.81280.24761.13690.49230.30612.7146-0.1490.89860.1044-0.44020.11060.2436-0.2065-0.04890.05590.6067-0.0781-0.13620.88590.12660.3747-29.71122.5003-85.8289
81.187-0.23390.89490.9852-0.59622.87340.09440.339-0.2567-0.26120.0404-0.02320.3180.1698-0.14620.24240.01040.03850.3008-0.0610.3620.7872-19.6802-54.1559
92.54410.8676-0.73733.0245-0.68962.5760.1259-0.1829-0.00630.3812-0.0159-0.0211-0.15250.0908-0.08540.18780.02710.0030.15880.00280.28927.5396-12.7849-28.0645
101.55120.11610.35090.12350.28331.8153-0.06121.0333-0.2081-0.44090.14350.026-0.04930.2936-0.06890.7534-0.1103-0.02630.9587-0.09570.2778-9.918-12.5909-84.6671
110.6213-0.38731.83760.13950.21544.97820.43360.3076-0.3075-0.40320.04720.06751.440.2342-0.39450.9633-0.0477-0.16520.4916-0.04920.557728.5144-79.2365-62.2069
122.44510.25720.26772.253-0.07143.09910.2101-0.005-0.2160.02850.0623-0.28030.61720.3551-0.19390.32840.0931-0.0680.1801-0.02230.462638.5767-72.3759-30.7465
130.8628-0.00990.5613-0.10860.57462.89430.23810.5289-0.1984-0.24940.1223-0.0570.51930.5596-0.30661.04110.0531-0.1080.7106-0.1030.398323.1262-70.7356-91.0634
140.09630.60320.48220.98850.63062.9215-0.06550.41140.0609-0.51170.0996-0.1987-0.20970.2755-0.02380.44930.10330.08630.5523-0.0060.405438.4699-40.6628-64.1968
152.560.24660.0732.7915-0.47212.53060.117-0.1841-0.08070.2852-0.1292-0.2409-0.0580.07510.01710.1949-0.0086-0.01770.1526-0.00320.347833.7323-37.1394-31.3132
160.19320.22130.191.4045-0.35911.926-0.2130.39110.0949-0.79530.1061-0.1351-0.12690.04340.04620.8515-0.01990.03270.70210.00440.323629.786-48.9167-84.1393
170.3148-0.1092-0.28690.22191.05755.1315-0.12280.79690.3969-2.26730.31330.33770.1403-0.0877-0.02271.896-0.3115-0.09851.19660.20440.702226.0668-42.6892-120.7548
180.81351.09130.96421.10961.10065.0223-0.52430.71120.3238-0.73740.3061-0.1826-0.87820.51780.13560.7149-0.17480.02230.62840.11340.3842.655119.2386-61.2872
192.96150.76430.41093.7376-0.16152.68260.005-0.32830.22070.391-0.1484-0.0074-0.32720.10930.12310.2975-0.036-0.02550.1877-0.00120.3939-1.010719.8445-27.9011
200.1720.69710.48161.9906-0.10620.824-0.57210.58960.1687-0.95080.47720.1103-0.8570.49690.16521.0308-0.2871-0.07510.9520.1650.3149-7.441112.6035-82.6624
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'E' and (resid 3 through 99 )E3 - 99
2X-RAY DIFFRACTION2chain 'E' and (resid 100 through 269 )E100 - 269
3X-RAY DIFFRACTION3chain 'E' and (resid 270 through 403 )E270 - 403
4X-RAY DIFFRACTION4chain 'E' and (resid 404 through 491 )E404 - 491
5X-RAY DIFFRACTION5chain 'F' and (resid 3 through 99 )F3 - 99
6X-RAY DIFFRACTION6chain 'F' and (resid 100 through 288 )F100 - 288
7X-RAY DIFFRACTION7chain 'F' and (resid 289 through 486 )F289 - 486
8X-RAY DIFFRACTION8chain 'A' and (resid 4 through 138 )A4 - 138
9X-RAY DIFFRACTION9chain 'A' and (resid 139 through 266 )A139 - 266
10X-RAY DIFFRACTION10chain 'A' and (resid 267 through 484 )A267 - 484
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 99 )B1 - 99
12X-RAY DIFFRACTION12chain 'B' and (resid 100 through 288 )B100 - 288
13X-RAY DIFFRACTION13chain 'B' and (resid 289 through 496 )B289 - 496
14X-RAY DIFFRACTION14chain 'C' and (resid 2 through 99 )C2 - 99
15X-RAY DIFFRACTION15chain 'C' and (resid 100 through 288 )C100 - 288
16X-RAY DIFFRACTION16chain 'C' and (resid 289 through 452 )C289 - 452
17X-RAY DIFFRACTION17chain 'C' and (resid 453 through 486 )C453 - 486
18X-RAY DIFFRACTION18chain 'D' and (resid 7 through 99 )D7 - 99
19X-RAY DIFFRACTION19chain 'D' and (resid 100 through 269 )D100 - 269
20X-RAY DIFFRACTION20chain 'D' and (resid 270 through 486 )D270 - 486

+
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