[English] 日本語
Yorodumi
- PDB-7lmv: SPECIFIC INHIBITOR OF INTEGRIN ALPHA-V BETA-6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lmv
TitleSPECIFIC INHIBITOR OF INTEGRIN ALPHA-V BETA-6
ComponentsIntegrin inhibitor
KeywordsDE NOVO PROTEIN / de novo design / inhibitor / integrin / fibrosis
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDong, X. / Bera, A.K. / Roy, A. / Shi, L. / Springer, T.A. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Commun / Year: 2023
Title: De novo design of highly selective miniprotein inhibitors of integrins αvβ6 and αvβ8.
Authors: Anindya Roy / Lei Shi / Ashley Chang / Xianchi Dong / Andres Fernandez / John C Kraft / Jing Li / Viet Q Le / Rebecca Viazzo Winegar / Gerald Maxwell Cherf / Dean Slocum / P Daniel Poulson / ...Authors: Anindya Roy / Lei Shi / Ashley Chang / Xianchi Dong / Andres Fernandez / John C Kraft / Jing Li / Viet Q Le / Rebecca Viazzo Winegar / Gerald Maxwell Cherf / Dean Slocum / P Daniel Poulson / Garrett E Casper / Mary L Vallecillo-Zúniga / Jonard Corpuz Valdoz / Marcos C Miranda / Hua Bai / Yakov Kipnis / Audrey Olshefsky / Tanu Priya / Lauren Carter / Rashmi Ravichandran / Cameron M Chow / Max R Johnson / Suna Cheng / McKaela Smith / Catherine Overed-Sayer / Donna K Finch / David Lowe / Asim K Bera / Gustavo Matute-Bello / Timothy P Birkland / Frank DiMaio / Ganesh Raghu / Jennifer R Cochran / Lance J Stewart / Melody G Campbell / Pam M Van Ry / Timothy Springer / David Baker /
Abstract: The RGD (Arg-Gly-Asp)-binding integrins αvβ6 and αvβ8 are clinically validated cancer and fibrosis targets of considerable therapeutic importance. Compounds that can discriminate between ...The RGD (Arg-Gly-Asp)-binding integrins αvβ6 and αvβ8 are clinically validated cancer and fibrosis targets of considerable therapeutic importance. Compounds that can discriminate between homologous αvβ6 and αvβ8 and other RGD integrins, stabilize specific conformational states, and have high thermal stability could have considerable therapeutic utility. Existing small molecule and antibody inhibitors do not have all these properties, and hence new approaches are needed. Here we describe a generalized method for computationally designing RGD-containing miniproteins selective for a single RGD integrin heterodimer and conformational state. We design hyperstable, selective αvβ6 and αvβ8 inhibitors that bind with picomolar affinity. CryoEM structures of the designed inhibitor-integrin complexes are very close to the computational design models, and show that the inhibitors stabilize specific conformational states of the αvβ6 and the αvβ8 integrins. In a lung fibrosis mouse model, the αvβ6 inhibitor potently reduced fibrotic burden and improved overall lung mechanics, demonstrating the therapeutic potential of de novo designed integrin binding proteins with high selectivity.
History
DepositionFeb 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integrin inhibitor
B: Integrin inhibitor
C: Integrin inhibitor
D: Integrin inhibitor
E: Integrin inhibitor
F: Integrin inhibitor
G: Integrin inhibitor
H: Integrin inhibitor
I: Integrin inhibitor
J: Integrin inhibitor
K: Integrin inhibitor
L: Integrin inhibitor


Theoretical massNumber of molelcules
Total (without water)93,35912
Polymers93,35912
Non-polymers00
Water5,963331
1
A: Integrin inhibitor


Theoretical massNumber of molelcules
Total (without water)7,7801
Polymers7,7801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Integrin inhibitor


Theoretical massNumber of molelcules
Total (without water)7,7801
Polymers7,7801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Integrin inhibitor


Theoretical massNumber of molelcules
Total (without water)7,7801
Polymers7,7801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Integrin inhibitor


Theoretical massNumber of molelcules
Total (without water)7,7801
Polymers7,7801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Integrin inhibitor


Theoretical massNumber of molelcules
Total (without water)7,7801
Polymers7,7801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Integrin inhibitor


Theoretical massNumber of molelcules
Total (without water)7,7801
Polymers7,7801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Integrin inhibitor


Theoretical massNumber of molelcules
Total (without water)7,7801
Polymers7,7801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Integrin inhibitor


Theoretical massNumber of molelcules
Total (without water)7,7801
Polymers7,7801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Integrin inhibitor


Theoretical massNumber of molelcules
Total (without water)7,7801
Polymers7,7801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Integrin inhibitor


Theoretical massNumber of molelcules
Total (without water)7,7801
Polymers7,7801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Integrin inhibitor


Theoretical massNumber of molelcules
Total (without water)7,7801
Polymers7,7801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Integrin inhibitor


Theoretical massNumber of molelcules
Total (without water)7,7801
Polymers7,7801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.270, 92.270, 82.420
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

-
Components

#1: Protein
Integrin inhibitor


Mass: 7779.935 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.17 Å3/Da / Density % sol: 43.31 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / Details: 0.2 M KNO3, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0322 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0322 Å / Relative weight: 1
ReflectionResolution: 1.9→40.26 Å / Num. obs: 61653 / % possible obs: 99.99 % / Redundancy: 5.6 % / Biso Wilson estimate: 26.21 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.093 / Net I/σ(I): 10.4
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.613 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3570 / CC1/2: 0.114 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.18rc2_3793refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Designed Model

Resolution: 1.9→40.26 Å / SU ML: 0.2423 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 34.9264
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2678 1475 2.39 %
Rwork0.221 60178 -
obs0.2222 61653 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6374 0 0 334 6708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00576491
X-RAY DIFFRACTIONf_angle_d0.68438724
X-RAY DIFFRACTIONf_chiral_restr0.0499971
X-RAY DIFFRACTIONf_plane_restr0.00411128
X-RAY DIFFRACTIONf_dihedral_angle_d11.63662450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.960.34621360.28285498X-RAY DIFFRACTION99.77
1.96-2.030.31381340.25875462X-RAY DIFFRACTION99.66
2.03-2.110.35341340.22225472X-RAY DIFFRACTION99.8
2.11-2.210.2591340.23715448X-RAY DIFFRACTION99.73
2.21-2.330.3161340.26265479X-RAY DIFFRACTION99.73
2.33-2.470.31731400.27835467X-RAY DIFFRACTION99.82
2.47-2.660.24271400.25515481X-RAY DIFFRACTION99.77
2.66-2.930.28041310.25245485X-RAY DIFFRACTION99.93
2.93-3.350.29771280.23095494X-RAY DIFFRACTION99.98
3.35-4.220.29511320.17745494X-RAY DIFFRACTION99.82
4.22-40.260.18011320.18135398X-RAY DIFFRACTION98.5
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.550415110861.56164353517-0.356046229685.415646777252.029758699527.77908281725-0.106206001445-0.117367567683-0.0374631448454-0.21647286543-0.0185429511277-0.133827074174-0.25890141695-0.05517787869750.1003036780080.12011837476-0.01285524051870.02831644170260.1652625679860.0411997898240.15605147002930.545-17.319-0.726
24.293359900571.03759462751-0.0848806049996.33069496750.3916981260222.853796888-0.7701533384690.585968572878-0.519276974923-0.7808016655050.471928866744-0.3031439759820.737067711264-0.07873941457230.2717989990420.396924566829-0.0900309376040.1692860994540.248780123978-0.01659201643320.29116606292133.23-20.43-9.084
36.23605319113-0.333705070838-0.4920669970675.755077006264.003079277638.77736096584-0.4203335650510.669828647873-1.21601303633-0.833139192330.04327055099920.252312235303-0.00743276242862-0.1563866604440.2930937057170.722118673243-0.202492600362-0.002402655461350.314081319738-0.001954518571860.52715700810223.118-27.589-7.217
41.2396246578-0.6331484129831.224125082242.98874248978-0.04265120417477.98481882392-0.5010920013460.595654038933-0.418991358425-0.2764237914440.2468414113090.307448461177-0.307932161603-0.6503215948980.159516025770.22922662418-0.1882626730910.004170378524020.2783631008130.03077497468550.2266384841522.315-19.441-7.456
54.16064590120.274116172873-0.8278661784863.86794564223-1.952152577568.873175742860.0542722399974-0.2771680729640.162680121989-0.1153954859840.02925361164420.02746416239480.5029612234250.00598232207285-0.06461210377080.376816640249-0.03893119270540.005154989588090.222501969456-0.03421393152790.245288241363-28.3417.31141.794
64.86754615031.689825957-0.9743422126852.70233195895-0.3080252146495.80989652362-0.01099193796870.1640046638320.955147235423-0.438264231337-0.1782048869960.4453350808370.0583047688132-0.2709337430160.2235469615190.352161063156-0.00178263928463-0.02572627905650.2224040592250.01640469233610.437864600588-32.18120.35233.546
75.10011931930.5491176499360.2066101177394.216969136670.1646011245535.439183987870.248357524141-0.04773561494730.813412463840.5634722917660.05350468901850.346825946691-0.1423687597240.186488521589-0.2989800940260.463004483457-0.04447390959070.07971172146410.174961966934-0.002786189096990.28346257357-21.85223.43533.744
85.11340040035-0.07228739414821.885173500343.153798602741.52845588536.75616158913-0.03823313547230.182407888322-0.1678762928140.1188628292170.02984906163740.00487695259099-0.1551979288920.09874855312960.01103743529440.1130395726060.03185573456760.0471433508490.184970523119-0.005707275013280.18283035461346.415-8.495-14.425
94.85303995019-2.06011194553-0.2270084607144.666319358090.7624447327332.991382641090.2045707562981.08893018691-0.514276384398-0.391248802442-0.3878098284740.7050422284810.181874890739-0.6728067692010.1223608163120.253687744805-0.0329849933907-0.003671474342520.477410338582-0.08937568009340.30012892491541.032-10.491-22.146
103.19670664019-0.368279629967-0.3175084746844.959554408990.04407089537886.848511485510.2385158164330.603661207553-0.317933658735-0.285308241324-0.2751081880150.58759248388-0.678784756119-0.306009850373-0.06142976599880.1283975192190.05425278084480.02778959928670.3716297754740.003710097296860.21164728872640.506-2.78-22.053
113.418479264181.16328871884-2.338336397894.53619257988-2.16642264197.74585635533-0.123366063845-0.03449928863180.1262312910750.5349051452530.0801969850707-0.0447430631921-0.273925557213-0.6836562930090.004073267200150.250936111892-0.0112268424967-0.02935294208970.342551087235-0.04205505933940.216999005568-45.3296.63928.08
124.86959141012-0.3656044931090.8228340736794.97440623222-0.1587978998975.38310066211-0.3085422889740.08028052758530.5096203487490.05284014623660.0154365476084-0.327417915428-0.8111853643340.3832389495830.2913737815110.380370471445-0.0675299115118-0.08931790633860.286121689195-0.0001379949100180.322920590226-44.86214.37821.121
135.18176090239-1.529417238870.4454027028125.50714334649-1.338466555374.956907138740.2258582758730.28234309340.693736083310.257536414126-0.477975931634-0.533350538305-0.01302741166150.6842828955260.2310439785260.289516901705-0.09501463549340.02053222552540.524219288384-0.06504471920760.285014942185-38.5767.33820.382
143.302944874910.7300275533320.220843827956.7830092088-2.211336829958.46243724524-0.0994828117935-0.0872290055255-0.4957299050650.332947522259-0.454851850659-0.8311954582270.6140075250560.03912179003920.3587228887560.1416972117260.000349982606279-0.02973689075070.445887574154-0.08580629354420.220210646145-40.151.26719.112
152.43336698294-0.687085665072-1.234307962824.81727313559-1.695145482657.428544397760.378649822479-0.0985943789226-0.102705491909-0.339582929191-0.4456862467750.0608634824748-0.07472933927710.04803782755770.03817829541990.255357236567-0.0701877754311-0.03802968869660.369948255191-0.0234900869640.23557139024915.934-8.88-25.457
161.78784620797-2.252764462961.611704583267.050027256171.635688658797.430714375720.291878931209-0.4269132507280.1397765225810.664202167479-0.7352537402461.07496100778-0.0979013062958-1.225055849840.4415490256560.35570262105-0.04650294352690.09342231335950.463894385557-0.1248529106510.3498537379669.383-6.465-17.622
170.799797777199-0.48823249124-0.3965529092433.857549575420.5640438703280.855148867005-0.3789338791210.310117978707-0.0769323303865-0.03396555596910.1942507976650.836073119390.226077983971-0.3666276715960.2558239450640.344346927652-0.316307315634-0.06531548829740.6824399334970.1035177197050.42853713072912.634-15.54-17.685
180.60266638608-1.251069456850.7519196715833.69810609020.3507450076923.93451528708-0.1162302288080.743368005427-0.254772090771-0.4057792383360.1149028283860.3177706172360.00897728301826-0.256251063433-0.1274761378660.407130542061-0.332567862869-0.1142394994840.6592533039320.1783540288210.015911966585618.11-16.958-17.893
191.804862426740.2980094787860.4316674447354.76203023227-1.028277223496.451307888890.0752426999248-0.1355932074510.0233709606064-0.0149490526538-0.120258656897-0.341844012530.1874638628680.08228156813960.02070670883740.213292860619-0.04052006505010.02701322652380.224824244314-0.009847182569810.288522704245-14.1168.12717.699
200.542127360486-1.4257763070.7581296868883.97084053399-1.939888207192.16044192216-0.6231021519560.650810433501-0.185028240390.1237594250090.653878266777-1.43571107433-0.8138822925090.4714221750330.1130253041760.492217991925-0.2350269469960.08723334400620.508000978184-0.1324666071210.493329094081-12.37515.4423.343
214.237775240930.0237419872986-1.064607880634.532158980650.5738423311437.2070980253-0.3613539007360.6220321004270.1546608635140.1521519190810.674379080239-0.655552731243-0.1849888257260.0770484181531-0.2695551280250.440035706943-0.0928209932032-0.02097439148150.301331438246-0.07631806353860.241392464877-17.34616.60524.212
224.07189125610.7302531646291.806388666872.84266256458-0.8924814457648.18103643071-0.05054270362620.05030460104760.0800476658421-0.2319699484530.0917654587075-0.166571763814-0.0218230907784-0.223398785516-0.04436904824960.1671474090160.02501410743520.01652702775980.265093524833-0.01672146764410.245535837765-0.302-35.1651.967
237.186749593882.99065592069-4.039050058435.875721048181.263320894629.05384965106-0.142961756994-1.25238217351-1.351531834230.2896631399920.141534190858-1.018279622451.257238955360.7357874945960.07928295972120.361925569880.0496068020179-0.0256593818240.5214891966090.1033484918180.5888744986280.777-42.1549.683
241.24424305331.39263703572-0.2368757477423.42891265312-2.196805354313.494906481360.3600870483720.645150246803-0.9172293221390.0510975624856-0.737533526308-0.497165806552-0.1471605917940.8002140782660.3865093298050.2624765152570.106835216244-0.0610369076990.661052210575-0.09503859152170.5113249313977.159-34.9119.556
254.099089037842.2548805333-0.7019668242285.310144907791.994346214023.781123470660.5495305812360.384967221345-0.498931001377-0.163883101725-0.173166141355-0.645291030195-0.400499818921-0.124905055639-0.2340978595170.2763348192710.0532986389901-0.01296112929390.473840564924-0.01501361957710.2152544381965.786-29.1958.728
263.6151945836-0.876126353739-2.857399816523.042952989061.323067171842.7280102617-0.166708660456-0.192818681007-0.446485015140.155952086219-0.0008465067642750.0679976421940.7962484026180.1978843941620.1292390943480.1485512248890.0326268017758-0.02114019539080.2069790138640.01251979393490.220894470340.07628.256-37.149
273.32547045734-1.014176152890.6119238668984.086907592961.212654973524.41860529582-0.0240581909623-0.2684600453480.350628345272-0.217220170063-0.07307440997930.110743886204-0.586149244496-0.1216792948860.08000632514350.184397650015-0.00232270429947-0.030622857140.145437302061-0.0174058266480.184299395757-1.62338.837-39.179
285.784157980161.41566255549-0.9714825359344.12323540671.314592025875.275621268270.0510874397299-0.3101076206920.6807919506650.249275111860.0437391250720.485917210640.0270660879835-0.253661461614-0.08424765854020.1649871668880.0332036916522-0.0253986550690.2376313811480.01795302308830.244288568679-7.64733.788-32.75
295.026823150030.2393990917550.9089971712125.605413461571.799512571912.19488312068-0.0605240426229-0.909892104486-0.0405669906080.222188085505-0.208573990660.5086484791270.0831758522205-0.05004215508790.2395109614890.136005487096-0.0281956526156-0.007647963658290.2777863141170.04315667899770.230106250203-5.76928.781-29.813
302.449302544380.5145470222362.002387219824.819482830081.990212152418.12483470650.22344206543-0.05681094497470.16733272787-0.0840954361591-0.327280124094-0.07688718284320.403289174466-0.1597893012220.09347473161220.228671203166-0.05931995968660.040895363950.3128730589810.01637746287070.244077174634-15.932-44.41515.726
312.69321044284-0.3429468611780.2540580627887.837824963581.401034617796.524691589330.642247018428-0.1546742484390.2092687245771.01863200496-0.486239992843-0.7762435752310.5253967664550.596647658217-0.01019732725030.384860409639-0.0950346502056-0.01926842553530.4534378000090.0140253267740.367637081458-11.885-45.13924.234
322.563264730410.7962917053090.5871068265593.033512802220.3321328388281.50193682149-0.2311664615560.2009926602280.507054474878-0.3075774774780.369695794263-0.764300341127-0.03719390135010.2255337246510.06029882316520.368423801151-0.7080129569740.07010620292160.789517435372-0.1170628470740.392965638995-10.998-32.56222.357
332.25880392192-0.699168270244-1.427781136584.64961683972-1.352722914882.05671079643-0.1156803714480.229210866272-0.09244499036570.07299100997750.00226318657783-0.140901836077-0.123496027516-0.02612983649340.1082016185550.298329005935-0.1516398498550.03624603998750.428280257591-0.07154959410220.215319205204-18.011-36.45723.432
344.621628782290.781271701479-3.509559345263.24598008551-1.470617592912.98564865735-0.227472111032-0.0742557127537-0.1059410864550.02734061896410.0980795237458-0.3332418342160.5640951457130.3522590622450.06479341432870.200679283374-0.0571066452777-0.03340030259070.189023332247-0.01392411709250.19522565959821.69840.828-23.43
355.09034903305-0.34414016629-1.111452785533.333979655862.180789410925.772491849140.1334761394930.228905282660.04026863555640.0701355419545-0.3024554403250.370997582548-0.164111302891-0.7980810616210.1647608345790.1698917885810.0185692757006-0.003547143525780.180494197695-0.02219316121110.18175943358212.16344.601-25.723
364.310141215990.0801651220574-1.996953635215.569577693820.3574499423044.576711779250.14365118531-0.208646460063-0.1224960142360.412906042239-0.1826447244510.7653781215840.275996854229-0.2100299343340.04977192503260.217863495783-0.0787618482012-0.01294907353960.211773318437-0.004473637008760.22237611339613.00936.951-19.036
374.24802600191-0.229960690648-2.276519363654.427510178312.006137113262.86233780593-0.13608691291-0.295307387878-0.6641316759660.443128005478-0.5782774886850.1253406449-0.07844899917670.3810385435750.6336961766860.192556582561-0.0322141350514-0.05044079580440.1408031503280.0003158878943480.24899715083419.15335.382-17.871
384.03179961240.694535013029-4.122190087313.96808571137-2.751106693499.62239519411-0.137163840501-0.2370902743250.03384528744690.1005948267540.101001307495-0.02218217289360.903677749236-0.5766196054150.02037033204320.332628403925-0.2000636507820.004916699984370.449920726313-0.06091860081780.23483486712-0.122-25.06824.672
399.561760249365.75698865509-3.599156375869.76976527002-3.544042091486.96766618860.398583624411-0.9162002086470.4895244290710.202181221305-0.3445153182670.0677720693781-0.1795092303710.252871679029-0.05117267203620.3253607849470.0392975815445-0.04089779630840.403057283451-0.01953586597940.2749253882731.496-16.46730.502
405.54083179021-0.518613971972-0.5611219376373.716758708160.7792189375994.70481506173-0.2635398568090.3575936747540.507180454184-0.370714035395-0.008641544559-0.746821274179-0.216359942573-0.02833424356110.25733813010.259952686973-0.04530527783280.00560284866580.4338356233020.06479851066970.4100798991551.52-15.22819.826
415.48274183642-0.884930629408-0.2294006472115.247920653490.02265202931046.89448373640.32176581968-0.5244010574050.8142056657750.3056793980620.119792017994-0.664677926168-0.07978704197030.180407368703-0.3842635013850.203641940571-0.07814315630070.03263585662490.42649883093-0.09001381971860.3236734721169.562-22.82220.5
424.255168294081.18749551242.946601783084.124255919142.869318083413.8024309399-0.206803512135-0.5605357921450.264705812355-0.01690791658110.104340585756-0.0739154410477-1.132578842020.336051839575-0.02989672130130.320580692867-0.1504219709-0.03004993803270.4116822489970.1082674956350.1909689385090.14724.908-16.613
435.013300334275.045784532791.499366211285.371679163062.908931181028.122916514090.344704549141-0.672671504367-0.1379494864070.737882973154-0.3061486073190.2197754101110.6557795357140.2913612543340.01390233427360.3088607328520.04210571364840.01313108394510.3078374008210.02940209959490.326550491282-1.50716.435-10.652
449.76750351326-0.625630810727-2.80759367474.93298789454-0.8247392028947.85427351712-0.313999296577-0.0923900059374-1.33239961038-0.1603345464080.2056977513430.127261871331.40198083334-0.4708623524110.04447966275420.513131643932-0.0158899541440.0733588709280.28634053748-0.002177525290540.395793883706-1.27512.251-20.075
454.6980430691-1.01333781737-0.877413637464.688304399521.992815514935.310893559750.2860658406940.156318360591-0.5263657157550.112708842485-0.5482358810850.3774022575920.141171370019-0.9659619291860.2394228558950.303113280463-0.079849968837-0.02009085314320.485213319230.05410017236760.251239366953-7.61219.391-20.897
464.94612535422-0.390236233056-0.303108963346.362864387291.834415762667.5687656233-0.200340866378-0.3029935828140.1238235439960.256807666401-0.3407525242260.73329821514-0.345569596627-0.1053665961440.3808886041570.118840684894-0.01881842295050.0274201761590.2818686674320.07905889410460.187238363151-5.85924.279-23.822
47-0.02813822840490.02717474131670.00474021433579-0.0607499587548-0.05389678931260.02315218882680.003245492591160.0117186416490.004459898122990.003790812399620.002826004068070.01867805047330.0306633751895-0.0118052222141-0.01330423605750.251073398149-0.04072187774110.01351339985620.251689438679-0.003601870768070.2155119020941.1662.761-0.173
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 0:25 )A0 - 25
2X-RAY DIFFRACTION2( CHAIN A AND RESID 26:44 )A26 - 44
3X-RAY DIFFRACTION3( CHAIN A AND RESID 45:54 )A45 - 54
4X-RAY DIFFRACTION4( CHAIN A AND RESID 55:65 )A55 - 65
5X-RAY DIFFRACTION5( CHAIN B AND RESID 0:25 )B0 - 25
6X-RAY DIFFRACTION6( CHAIN B AND RESID 26:44 )B26 - 44
7X-RAY DIFFRACTION7( CHAIN B AND RESID 45:66 )B45 - 66
8X-RAY DIFFRACTION8( CHAIN C AND RESID 0:25 )C0 - 25
9X-RAY DIFFRACTION9( CHAIN C AND RESID 26:54 )C26 - 54
10X-RAY DIFFRACTION10( CHAIN C AND RESID 55:66 )C55 - 66
11X-RAY DIFFRACTION11( CHAIN D AND RESID 0:25 )D0 - 25
12X-RAY DIFFRACTION12( CHAIN D AND RESID 26:34 )D26 - 34
13X-RAY DIFFRACTION13( CHAIN D AND RESID 35:55 )D35 - 55
14X-RAY DIFFRACTION14( CHAIN D AND RESID 56:65 )D56 - 65
15X-RAY DIFFRACTION15( CHAIN E AND RESID 0:25 )E0 - 25
16X-RAY DIFFRACTION16( CHAIN E AND RESID 26:34 )E26 - 34
17X-RAY DIFFRACTION17( CHAIN E AND RESID 35:54 )E35 - 54
18X-RAY DIFFRACTION18( CHAIN E AND RESID 55:66 )E55 - 66
19X-RAY DIFFRACTION19( CHAIN F AND RESID 0:34 )F0 - 34
20X-RAY DIFFRACTION20( CHAIN F AND RESID 35:54 )F35 - 54
21X-RAY DIFFRACTION21( CHAIN F AND RESID 55:67 )F55 - 67
22X-RAY DIFFRACTION22( CHAIN G AND RESID 0:25 )G0 - 25
23X-RAY DIFFRACTION23( CHAIN G AND RESID 26:34 )G26 - 34
24X-RAY DIFFRACTION24( CHAIN G AND RESID 35:54 )G35 - 54
25X-RAY DIFFRACTION25( CHAIN G AND RESID 55:65 )G55 - 65
26X-RAY DIFFRACTION26( CHAIN H AND RESID 0:10 )H0 - 10
27X-RAY DIFFRACTION27( CHAIN H AND RESID 11:34 )H11 - 34
28X-RAY DIFFRACTION28( CHAIN H AND RESID 35:55 )H35 - 55
29X-RAY DIFFRACTION29( CHAIN H AND RESID 56:67 )H56 - 67
30X-RAY DIFFRACTION30( CHAIN I AND RESID 0:25 )I0 - 25
31X-RAY DIFFRACTION31( CHAIN I AND RESID 26:44 )I26 - 44
32X-RAY DIFFRACTION32( CHAIN I AND RESID 45:54 )I45 - 54
33X-RAY DIFFRACTION33( CHAIN I AND RESID 55:66 )I55 - 66
34X-RAY DIFFRACTION34( CHAIN J AND RESID 0:10 )J0 - 10
35X-RAY DIFFRACTION35( CHAIN J AND RESID 11:34 )J11 - 34
36X-RAY DIFFRACTION36( CHAIN J AND RESID 35:55 )J35 - 55
37X-RAY DIFFRACTION37( CHAIN J AND RESID 56:65 )J56 - 65
38X-RAY DIFFRACTION38( CHAIN K AND RESID 0:10 )K0 - 10
39X-RAY DIFFRACTION39( CHAIN K AND RESID 11:25 )K11 - 25
40X-RAY DIFFRACTION40( CHAIN K AND RESID 26:44 )K26 - 44
41X-RAY DIFFRACTION41( CHAIN K AND RESID 45:65 )K45 - 65
42X-RAY DIFFRACTION42( CHAIN L AND RESID 0:10 )L0 - 10
43X-RAY DIFFRACTION43( CHAIN L AND RESID 11:25 )L11 - 25
44X-RAY DIFFRACTION44( CHAIN L AND RESID 26:34 )L26 - 34
45X-RAY DIFFRACTION45( CHAIN L AND RESID 35:55 )L35 - 55
46X-RAY DIFFRACTION46( CHAIN L AND RESID 56:67 )L56 - 67
47X-RAY DIFFRACTION47( CHAIN A AND RESID 101:127 ) OR ( CHAIN B AND RESID 101:125 ) OR ( CHAIN C AND RESID 101:131 ) OR ( CHAIN D AND RESID 101:135 ) OR ( CHAIN E AND RESID 101:127 ) OR ( CHAIN F AND RESID 101:121 ) OR ( CHAIN G AND RESID 101:120 ) OR ( CHAIN H AND RESID 101:137 ) OR ( CHAIN I AND RESID 101:123 ) OR ( CHAIN J AND RESID 101:132 ) OR ( CHAIN K AND RESID 101:132 ) OR ( CHAIN L AND RESID 101:121 )A101 - 127
48X-RAY DIFFRACTION47( CHAIN A AND RESID 101:127 ) OR ( CHAIN B AND RESID 101:125 ) OR ( CHAIN C AND RESID 101:131 ) OR ( CHAIN D AND RESID 101:135 ) OR ( CHAIN E AND RESID 101:127 ) OR ( CHAIN F AND RESID 101:121 ) OR ( CHAIN G AND RESID 101:120 ) OR ( CHAIN H AND RESID 101:137 ) OR ( CHAIN I AND RESID 101:123 ) OR ( CHAIN J AND RESID 101:132 ) OR ( CHAIN K AND RESID 101:132 ) OR ( CHAIN L AND RESID 101:121 )B101 - 125
49X-RAY DIFFRACTION47( CHAIN A AND RESID 101:127 ) OR ( CHAIN B AND RESID 101:125 ) OR ( CHAIN C AND RESID 101:131 ) OR ( CHAIN D AND RESID 101:135 ) OR ( CHAIN E AND RESID 101:127 ) OR ( CHAIN F AND RESID 101:121 ) OR ( CHAIN G AND RESID 101:120 ) OR ( CHAIN H AND RESID 101:137 ) OR ( CHAIN I AND RESID 101:123 ) OR ( CHAIN J AND RESID 101:132 ) OR ( CHAIN K AND RESID 101:132 ) OR ( CHAIN L AND RESID 101:121 )C101 - 131
50X-RAY DIFFRACTION47( CHAIN A AND RESID 101:127 ) OR ( CHAIN B AND RESID 101:125 ) OR ( CHAIN C AND RESID 101:131 ) OR ( CHAIN D AND RESID 101:135 ) OR ( CHAIN E AND RESID 101:127 ) OR ( CHAIN F AND RESID 101:121 ) OR ( CHAIN G AND RESID 101:120 ) OR ( CHAIN H AND RESID 101:137 ) OR ( CHAIN I AND RESID 101:123 ) OR ( CHAIN J AND RESID 101:132 ) OR ( CHAIN K AND RESID 101:132 ) OR ( CHAIN L AND RESID 101:121 )D101 - 135
51X-RAY DIFFRACTION47( CHAIN A AND RESID 101:127 ) OR ( CHAIN B AND RESID 101:125 ) OR ( CHAIN C AND RESID 101:131 ) OR ( CHAIN D AND RESID 101:135 ) OR ( CHAIN E AND RESID 101:127 ) OR ( CHAIN F AND RESID 101:121 ) OR ( CHAIN G AND RESID 101:120 ) OR ( CHAIN H AND RESID 101:137 ) OR ( CHAIN I AND RESID 101:123 ) OR ( CHAIN J AND RESID 101:132 ) OR ( CHAIN K AND RESID 101:132 ) OR ( CHAIN L AND RESID 101:121 )E101 - 127
52X-RAY DIFFRACTION47( CHAIN A AND RESID 101:127 ) OR ( CHAIN B AND RESID 101:125 ) OR ( CHAIN C AND RESID 101:131 ) OR ( CHAIN D AND RESID 101:135 ) OR ( CHAIN E AND RESID 101:127 ) OR ( CHAIN F AND RESID 101:121 ) OR ( CHAIN G AND RESID 101:120 ) OR ( CHAIN H AND RESID 101:137 ) OR ( CHAIN I AND RESID 101:123 ) OR ( CHAIN J AND RESID 101:132 ) OR ( CHAIN K AND RESID 101:132 ) OR ( CHAIN L AND RESID 101:121 )F101 - 121
53X-RAY DIFFRACTION47( CHAIN A AND RESID 101:127 ) OR ( CHAIN B AND RESID 101:125 ) OR ( CHAIN C AND RESID 101:131 ) OR ( CHAIN D AND RESID 101:135 ) OR ( CHAIN E AND RESID 101:127 ) OR ( CHAIN F AND RESID 101:121 ) OR ( CHAIN G AND RESID 101:120 ) OR ( CHAIN H AND RESID 101:137 ) OR ( CHAIN I AND RESID 101:123 ) OR ( CHAIN J AND RESID 101:132 ) OR ( CHAIN K AND RESID 101:132 ) OR ( CHAIN L AND RESID 101:121 )G101 - 120
54X-RAY DIFFRACTION47( CHAIN A AND RESID 101:127 ) OR ( CHAIN B AND RESID 101:125 ) OR ( CHAIN C AND RESID 101:131 ) OR ( CHAIN D AND RESID 101:135 ) OR ( CHAIN E AND RESID 101:127 ) OR ( CHAIN F AND RESID 101:121 ) OR ( CHAIN G AND RESID 101:120 ) OR ( CHAIN H AND RESID 101:137 ) OR ( CHAIN I AND RESID 101:123 ) OR ( CHAIN J AND RESID 101:132 ) OR ( CHAIN K AND RESID 101:132 ) OR ( CHAIN L AND RESID 101:121 )H101 - 137
55X-RAY DIFFRACTION47( CHAIN A AND RESID 101:127 ) OR ( CHAIN B AND RESID 101:125 ) OR ( CHAIN C AND RESID 101:131 ) OR ( CHAIN D AND RESID 101:135 ) OR ( CHAIN E AND RESID 101:127 ) OR ( CHAIN F AND RESID 101:121 ) OR ( CHAIN G AND RESID 101:120 ) OR ( CHAIN H AND RESID 101:137 ) OR ( CHAIN I AND RESID 101:123 ) OR ( CHAIN J AND RESID 101:132 ) OR ( CHAIN K AND RESID 101:132 ) OR ( CHAIN L AND RESID 101:121 )I101 - 123
56X-RAY DIFFRACTION47( CHAIN A AND RESID 101:127 ) OR ( CHAIN B AND RESID 101:125 ) OR ( CHAIN C AND RESID 101:131 ) OR ( CHAIN D AND RESID 101:135 ) OR ( CHAIN E AND RESID 101:127 ) OR ( CHAIN F AND RESID 101:121 ) OR ( CHAIN G AND RESID 101:120 ) OR ( CHAIN H AND RESID 101:137 ) OR ( CHAIN I AND RESID 101:123 ) OR ( CHAIN J AND RESID 101:132 ) OR ( CHAIN K AND RESID 101:132 ) OR ( CHAIN L AND RESID 101:121 )J101 - 132
57X-RAY DIFFRACTION47( CHAIN A AND RESID 101:127 ) OR ( CHAIN B AND RESID 101:125 ) OR ( CHAIN C AND RESID 101:131 ) OR ( CHAIN D AND RESID 101:135 ) OR ( CHAIN E AND RESID 101:127 ) OR ( CHAIN F AND RESID 101:121 ) OR ( CHAIN G AND RESID 101:120 ) OR ( CHAIN H AND RESID 101:137 ) OR ( CHAIN I AND RESID 101:123 ) OR ( CHAIN J AND RESID 101:132 ) OR ( CHAIN K AND RESID 101:132 ) OR ( CHAIN L AND RESID 101:121 )K101 - 132
58X-RAY DIFFRACTION47( CHAIN A AND RESID 101:127 ) OR ( CHAIN B AND RESID 101:125 ) OR ( CHAIN C AND RESID 101:131 ) OR ( CHAIN D AND RESID 101:135 ) OR ( CHAIN E AND RESID 101:127 ) OR ( CHAIN F AND RESID 101:121 ) OR ( CHAIN G AND RESID 101:120 ) OR ( CHAIN H AND RESID 101:137 ) OR ( CHAIN I AND RESID 101:123 ) OR ( CHAIN J AND RESID 101:132 ) OR ( CHAIN K AND RESID 101:132 ) OR ( CHAIN L AND RESID 101:121 )L101 - 121

+
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