[English] 日本語
Yorodumi
- PDB-6sb4: Crystal structure of murine perforin-2 P2 domain crystal form 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sb4
TitleCrystal structure of murine perforin-2 P2 domain crystal form 2
ComponentsMacrophage-expressed gene 1 protein
KeywordsTOXIN / pore-forming protein / P2 domain / membrane binding / beta-hairpin
Function / homology
Function and homology information


dendritic cell antigen processing and presentation / antigen processing and presentation of exogenous peptide antigen / phagolysosome membrane / endolysosome / pore-forming activity / antibacterial innate immune response / wide pore channel activity / antigen processing and presentation of exogenous peptide antigen via MHC class I / phagocytic vesicle / phagocytic vesicle membrane ...dendritic cell antigen processing and presentation / antigen processing and presentation of exogenous peptide antigen / phagolysosome membrane / endolysosome / pore-forming activity / antibacterial innate immune response / wide pore channel activity / antigen processing and presentation of exogenous peptide antigen via MHC class I / phagocytic vesicle / phagocytic vesicle membrane / cytoplasmic vesicle / defense response to Gram-negative bacterium / adaptive immune response / defense response to Gram-positive bacterium / defense response to bacterium
Similarity search - Function
Macrophage-expressed gene 1 protein / membrane-attack complex / perforin / Membrane attack complex/perforin (MACPF) domain profile. / MAC/Perforin domain / Membrane attack complex component/perforin (MACPF) domain
Similarity search - Domain/homology
Macrophage-expressed gene 1 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 Å
AuthorsNi, T. / Yu, X. / Ginger, L. / Gilbert, R.J.C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N000331/1 United Kingdom
CitationJournal: Sci Adv / Year: 2020
Title: Structure and mechanism of bactericidal mammalian perforin-2, an ancient agent of innate immunity.
Authors: Tao Ni / Fang Jiao / Xiulian Yu / Saša Aden / Lucy Ginger / Sophie I Williams / Fangfang Bai / Vojtěch Pražák / Dimple Karia / Phillip Stansfeld / Peijun Zhang / George Munson / Gregor ...Authors: Tao Ni / Fang Jiao / Xiulian Yu / Saša Aden / Lucy Ginger / Sophie I Williams / Fangfang Bai / Vojtěch Pražák / Dimple Karia / Phillip Stansfeld / Peijun Zhang / George Munson / Gregor Anderluh / Simon Scheuring / Robert J C Gilbert /
Abstract: Perforin-2 (MPEG1) is thought to enable the killing of invading microbes engulfed by macrophages and other phagocytes, forming pores in their membranes. Loss of perforin-2 renders individual ...Perforin-2 (MPEG1) is thought to enable the killing of invading microbes engulfed by macrophages and other phagocytes, forming pores in their membranes. Loss of perforin-2 renders individual phagocytes and whole organisms significantly more susceptible to bacterial pathogens. Here, we reveal the mechanism of perforin-2 activation and activity using atomic structures of pre-pore and pore assemblies, high-speed atomic force microscopy, and functional assays. Perforin-2 forms a pre-pore assembly in which its pore-forming domain points in the opposite direction to its membrane-targeting domain. Acidification then triggers pore formation, via a 180° conformational change. This novel and unexpected mechanism prevents premature bactericidal attack and may have played a key role in the evolution of all perforin family proteins.
History
DepositionJul 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Macrophage-expressed gene 1 protein
B: Macrophage-expressed gene 1 protein
C: Macrophage-expressed gene 1 protein
D: Macrophage-expressed gene 1 protein
E: Macrophage-expressed gene 1 protein
F: Macrophage-expressed gene 1 protein
G: Macrophage-expressed gene 1 protein
H: Macrophage-expressed gene 1 protein


Theoretical massNumber of molelcules
Total (without water)258,3658
Polymers258,3658
Non-polymers00
Water00
1
A: Macrophage-expressed gene 1 protein


Theoretical massNumber of molelcules
Total (without water)32,2961
Polymers32,2961
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Macrophage-expressed gene 1 protein


Theoretical massNumber of molelcules
Total (without water)32,2961
Polymers32,2961
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Macrophage-expressed gene 1 protein


Theoretical massNumber of molelcules
Total (without water)32,2961
Polymers32,2961
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Macrophage-expressed gene 1 protein


Theoretical massNumber of molelcules
Total (without water)32,2961
Polymers32,2961
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Macrophage-expressed gene 1 protein


Theoretical massNumber of molelcules
Total (without water)32,2961
Polymers32,2961
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Macrophage-expressed gene 1 protein


Theoretical massNumber of molelcules
Total (without water)32,2961
Polymers32,2961
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Macrophage-expressed gene 1 protein


Theoretical massNumber of molelcules
Total (without water)32,2961
Polymers32,2961
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Macrophage-expressed gene 1 protein


Theoretical massNumber of molelcules
Total (without water)32,2961
Polymers32,2961
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.230, 70.050, 128.140
Angle α, β, γ (deg.)78.500, 79.050, 85.010
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))A377 - 464
121(chain 'A' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))A473 - 538
131(chain 'A' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))A550 - 579
241(chain 'B' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))B377 - 464
251(chain 'B' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))B473 - 538
261(chain 'B' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))B550 - 579
371(chain 'C' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))C377 - 464
381(chain 'C' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))C473 - 538
391(chain 'C' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))C550 - 579
4101(chain 'D' and (resid 377 through 465 or resid 473 through 580))D377 - 464
4111(chain 'D' and (resid 377 through 465 or resid 473 through 580))D473 - 538
4121(chain 'D' and (resid 377 through 465 or resid 473 through 580))D550 - 579
5131(chain 'E' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))E377 - 464
5141(chain 'E' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))E473 - 538
5151(chain 'E' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))E550 - 579
6161(chain 'F' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))F377 - 464
6171(chain 'F' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))F473 - 538
6181(chain 'F' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))F550 - 579
7191(chain 'G' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))G377 - 464
7201(chain 'G' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))G473 - 538
7211(chain 'G' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))G550 - 579
8221(chain 'H' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))H377 - 464
8231(chain 'H' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))H473 - 538
8241(chain 'H' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))H550 - 579

-
Components

#1: Protein
Macrophage-expressed gene 1 protein / Mpg-1 / Perforin-2 / P-2 / Protein MPS1


Mass: 32295.625 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mpeg1 / Production host: Homo sapiens (human) / References: UniProt: A1L314

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.53 Å3/Da / Density % sol: 65.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M MES pH6.0 10% PEG6000, 40mM potassium sodium tartrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.17→56.09 Å / Num. obs: 37940 / % possible obs: 95.3 % / Redundancy: 10.7 % / Biso Wilson estimate: 73.77 Å2 / Net I/σ(I): 10.41
Reflection shellResolution: 3.17→3.28 Å / Num. unique obs: 2362

-
Processing

Software
NameVersionClassification
PHENIXdev_3488refinement
PHENIXdev_3488refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.17→56.09 Å / SU ML: 0.3529 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 24.2192
RfactorNum. reflection% reflection
Rfree0.2246 1975 5.21 %
Rwork0.1887 --
obs0.1906 37940 95.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 90.03 Å2
Refinement stepCycle: LAST / Resolution: 3.17→56.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11992 0 0 0 11992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002912282
X-RAY DIFFRACTIONf_angle_d0.763516606
X-RAY DIFFRACTIONf_chiral_restr0.04811824
X-RAY DIFFRACTIONf_plane_restr0.00532138
X-RAY DIFFRACTIONf_dihedral_angle_d3.16557225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.17-3.250.2923860.28021595X-RAY DIFFRACTION59.69
3.25-3.340.30861260.27642064X-RAY DIFFRACTION76.02
3.34-3.440.29421320.2392669X-RAY DIFFRACTION99.79
3.44-3.550.30641470.23482707X-RAY DIFFRACTION99.89
3.55-3.670.23931520.21822712X-RAY DIFFRACTION99.97
3.67-3.820.25111290.20192684X-RAY DIFFRACTION100
3.82-3.990.22491490.18942698X-RAY DIFFRACTION99.93
3.99-4.20.20821560.1872667X-RAY DIFFRACTION99.89
4.2-4.470.21931620.16582700X-RAY DIFFRACTION99.86
4.47-4.810.16481490.14382669X-RAY DIFFRACTION100
4.81-5.30.19531710.1582697X-RAY DIFFRACTION100
5.3-6.060.23221300.18162720X-RAY DIFFRACTION100
6.06-7.630.20491330.19262706X-RAY DIFFRACTION100
7.63-56.090.22421530.17992677X-RAY DIFFRACTION99.4
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)
13.53859653787-5.03557741171.997884659136.78027737502-2.225004600951.988436795030.4737993787090.206788007594-0.741280431632-0.177760503241-0.4107390172270.7781949192510.5887715398130.414273423367-0.1229524267920.6359812419310.01417445682170.03213713190290.536585873913-0.03839058170030.60603083913989.891387670342.294132243-17.2333636738
27.78479080323-0.4386476242510.08223443305794.49125812872-0.2819651146339.312976403910.1310652571940.2152201268570.102318817773-0.00595490580286-0.3800599764510.516269053192-0.652894822006-1.133918221510.2755707551480.4301778824870.1463621123820.03642035136260.437279916444-0.03216298051370.43960999826473.470898207662.2648870262-17.2274331397
39.07807119327-0.390468755001-1.16000207422.260558932074.47701851988.857481514820.4248047438660.6105552677610.5363959976070.206337499159-0.497708282387-0.0493028362515-0.440927864396-0.526504328978-0.04263949515620.5524754000950.0306810331527-0.01626269956970.4117706993470.1616862843610.42679310946598.655290927364.4473879008-8.42177740728
46.94845294461-2.675411853230.1996918492330.9851849314470.2039415934610.779024967465-0.256054958698-0.8245115251321.6356739755-1.012613850830.719090101346-1.03566666765-0.724898630732-0.0719897154307-0.3057960793460.99131555356-0.1258908372910.06409341170080.633871685521-0.0469126492240.75446364222994.938989506176.6116441226-1.15165405088
55.39358909931-1.334552624090.3544484039611.76801723041-2.144465480643.48090221425-0.02862782009080.2349234081220.4612816726040.0359506778072-0.0362674252009-0.245406666753-0.2935349505020.5664465492080.2607374123540.460824417533-0.03196574418760.03375032487820.4837079962910.001658649762990.381009835111104.27916728870.989192855-5.78435554561
67.4704146268-2.12866433642-0.01219164203754.732867379390.8506664817459.123249691680.0823239416017-0.0153814606917-0.835192641940.1125805975710.142929151861-0.3200488293681.129472691580.883138625878-0.08492866943430.633486707020.230693842245-0.07125804959920.522911440414-0.0730271141120.509845357886111.54539936453.9342568721-0.586997295992
78.696664588930.04299901712711.070519084243.066486509541.370779506036.640606507570.0714095688239-0.7421374830710.06753089316460.1871619268590.537982811940.2577088169910.774554403408-0.332771556464-0.6466197848060.5872619174540.03689643499420.0879511779090.4929566255170.2165746194220.478449551526105.18141313763.232202274124.2416938024
86.12170070601-0.06059710276643.277020861396.37692094781-1.467805167792.166270236451.148653786361.097426465030.953456907162-2.04643906787-0.6069283206570.513773838805-0.251081928649-1.36607080772-0.6635241961770.9329604341290.4125287719720.003295628226261.14842033190.2970905986590.89225063409698.594818732579.007395225823.3201318848
96.613488319621.66371328869-1.012634540175.332763377412.13709805196.07728741194-0.45502831720.628411985771-0.448528939221-0.03206627903490.2497451248460.0195337155310.342165124733-0.2836743591690.1703808115520.6112570663580.1399375388180.04126794980750.738429687236-0.06759880961930.468036705583102.9310065261.227358230117.9506576087
105.5703119652-6.18602540857-1.111105299987.95047758746-0.1019975571261.547847604790.26522150874-0.06467991700881.02131704474-0.8232706781510.187961433763-0.559967920722-0.623389960056-0.255684904719-0.3993527692070.8241037040550.05231515069510.02431473739710.5739230728690.03514742235990.66236701000496.286823219785.089146895726.9721377378
117.520132417882.676185715210.5782875185986.74509827934-0.07344948468459.2419890963-0.246979697760.232683410062-0.13024152787-0.0562483513530.305903696059-0.4348574641380.2214117660561.53242432941-0.06281297911550.4140233260250.1599100010970.1088028554070.6926947454670.08178882566790.36174471773117.4518533164.880402066421.0320740032
124.20414392859-0.337770712389-0.1747978553572.476805330323.138570313467.005686318210.301046333292-0.0977299719991-0.5966192991230.505619765659-0.150113834336-0.4877701283981.2698611871.19355861873-0.06594052765480.6263233206470.3238894952770.005967599707830.5820418406380.04299249576130.572932947861117.48217550158.74543412129.2473229517
134.1687428153-1.35241654713-1.413962589244.741057636371.844150970294.051109795730.2064639823520.4884671643670.8729545291440.581559050631-0.406110871260.0206258975868-0.5246817912920.1726943500960.2595143136140.606163035292-0.0403151415534-0.01425585997610.3642561636030.09789132106340.594469532574110.74628005182.299891969950.0652314503
146.66154584185-5.356514352220.8112248468129.33624961822-0.9764920064852.652230154470.344869161324-0.02635089088911.71768124148-0.513938438092-0.382264594632-0.567436995152-0.45640357621-0.712420556641-0.05738651593260.9307556936180.0153202272011-0.02851402393540.6284611027930.01523056742121.12091392204103.034721823100.19091370652.1828344827
158.22090146367-1.27296864809-0.9523026519067.595045224312.894546622783.997550675380.1449941060140.1266337555190.2906612612950.7380199453440.136758542037-1.391738835040.5767993973371.38234842225-0.2337664249570.5293902870630.0773216786386-0.1693335987070.706279215463-0.05655876855530.804494316873126.68036055571.994283568450.5889621026
166.782701403894.26057754317-2.844697449272.73058369232-1.749265201951.400984479920.461567721682-0.647146403142-0.560766165329-0.09832447707180.190125300893-0.1887063116840.1699356285110.947068644444-0.5670601720430.8422467134370.0144901814404-0.3860854431650.760235721488-0.02681218540050.812990590411131.07726841276.129355171456.9140392427
178.6089428173-1.403706189611.399364286050.225578117107-0.3379984470949.81404270869-0.1369042497830.0140055633323-0.309452256089-0.3747928991960.145259845467-0.3549566970790.6168885189970.4404724583620.00996857370170.636748516322-0.0860538488960.1029402929490.315514762309-0.0850908819030.591892485709105.08173347973.102223231569.8985977035
185.76301914069-5.016443181092.290213423757.22869703827-2.766127516171.7978859466-0.109455062593-0.830767617315-1.048477561560.2692595134930.2792781189130.4317994367710.352331008958-0.0578937069475-0.2425431951690.931694401-0.0748261382690.07831510013190.6379600698290.2123366754550.773448574764114.87369608357.415315767483.3261146425
196.880693685011.010698878021.530199416333.496077094551.322521833145.68864101934-0.306309094308-0.454659732080.6988813801860.0939394346086-0.14803536650.367672142203-0.910692806523-1.184554878120.432238904860.5919940424750.103845084214-0.008797133651530.524097623677-0.07434267220370.45837299639294.293057775182.63108505976.5794777318
208.55251967852-4.971434755921.320742193475.061975068610.3367012033473.775378144240.5648408230010.636563103839-1.13024374825-0.904019809324-0.3691309576780.06622875329091.02796521395-0.382552488442-0.2435879782161.1538559639-0.2464009663050.1017611167550.505230423791-0.2049361255060.82295539376195.468905697860.076525101444.7395999234
212.72258493817-3.132259954440.8591667078889.308701729480.07006258162350.09070368852980.145913128028-0.0912214446798-0.3238878094940.5856531914040.0909547561509-0.707665005430.3249033699250.18479962539-0.2478082493960.980985778876-0.1308763413460.07268213082060.662403304858-0.1039102352240.822260156057106.17847580247.846833208854.4157738005
225.9830322783-0.407037002203-0.9466530139688.68699080123-2.099823237713.793013238240.0005484720979030.0125215205409-0.535065321198-0.711086086988-0.03291003115031.236278740991.31649529858-1.311537303130.02835189774430.667762604307-0.3220274202180.07315320065731.04404434304-0.2290056624380.63142787536383.168069346565.763813789851.1701180554
237.60944430117-0.9224166202322.582302855236.66726716335-0.5730695767488.2826355768-0.2569598830690.1985556233210.0849998204957-0.403253577380.03892046484110.407900689242-0.481790374491-1.190363332130.2691027120210.554653196452-0.009803303814980.08928259569310.683738895637-0.1218916485170.38027490190887.086747044575.414203043850.635147098
244.93839089291-0.906713024941.024054269658.1921616384-5.531400155574.496687867460.06424632014830.43913719832-1.083788863750.220478548823-0.3305039023260.168711876151.116287153051.055760664130.201730170590.8533476105940.1979390169710.09690989922160.479631598963-0.09629419160460.63403340895986.210422651751.31165364425.66596835074
252.92774548282-5.175426090710.2227008785897.34174310762-0.4464647757661.06121066749-0.456744630651-0.192995795675-0.7628363676781.119557511790.5436578489520.423978892780.5445658674040.08016674088510.03224808246351.177083196330.1133268315170.05940290927330.5692559887560.08758733831680.89453153834591.596290402632.926824362513.3178066797
268.24987819665-1.542382618111.961444420793.542356921160.2751028066088.77477863846-0.441240494416-0.669823493313-0.3498865231290.8561296243340.2163255236720.606445506192-0.562474584563-0.7998951906070.2347910097190.6862020316460.1998004403150.310359100990.5314047271480.070845696990.68004049291972.638130821558.92008857711.2879489992
275.128060677850.2452497146571.555112639179.34662859032-1.900668787199.75367246910.144412168654-0.6272450276510.498756065778-0.799138555594-0.1130392189530.004604972610610.434927320368-1.56711596895-0.1747930569050.761861311280.2519544504420.2140150692861.087914486030.1665308434830.5873433179869.9761545757.511491695919.6736481155
288.33649381455-3.92088075046-0.2873320564062.573702842841.546220948065.468471418510.6824924462062.636905954980.887907834311-1.2564223374-0.6786834147610.329392777912-0.6826599769820.03926432155160.11144033120.799867224708-0.0326401565797-0.03194508889661.152481536190.3468949597230.7057004653298.664242348368.6763844593-38.7248963918
294.13358647136-4.91347462113-1.221081570299.376973573941.610192692480.7959394746910.0235469247633-0.002415150771010.88445581290.215776361302-0.0947746115579-0.520948311284-0.3412080462590.1364338455490.06622235216640.713900101997-0.171418738306-0.02932722296060.696832306339-0.04754240661170.69820203540591.815065875384.0749684913-26.7842174467
301.73844444227-1.095504141062.526394109350.685190022147-1.585384561673.670318497310.5503299596791.10835258517-2.03469230319-1.190845798190.570180550156-1.224180205550.00871734380278-0.530839554938-0.1685806044840.661066115728-0.105272916090.2684109993891.82267792326-0.6950629633541.38833171892107.18832199951.0377547621-46.8840439116
317.00281497097-1.53288269016-1.449170322656.293720274330.3096567267866.39624565442-0.2523239604551.308658141310.169415289566-0.4920507619130.192846674391-0.8880378235060.4262925178271.212703254510.1077255716750.4609049817260.06076319587620.01679738249451.23254317223-0.09507734522870.561097280792111.92369632260.0754390678-32.1019735091
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 377 through 463 )
2X-RAY DIFFRACTION2chain 'A' and (resid 464 through 581 )
3X-RAY DIFFRACTION3chain 'B' and (resid 376 through 412 )
4X-RAY DIFFRACTION4chain 'B' and (resid 413 through 435 )
5X-RAY DIFFRACTION5chain 'B' and (resid 436 through 511 )
6X-RAY DIFFRACTION6chain 'B' and (resid 512 through 579 )
7X-RAY DIFFRACTION7chain 'C' and (resid 376 through 387 )
8X-RAY DIFFRACTION8chain 'C' and (resid 388 through 397 )
9X-RAY DIFFRACTION9chain 'C' and (resid 398 through 412 )
10X-RAY DIFFRACTION10chain 'C' and (resid 413 through 464 )
11X-RAY DIFFRACTION11chain 'C' and (resid 465 through 511 )
12X-RAY DIFFRACTION12chain 'C' and (resid 512 through 579 )
13X-RAY DIFFRACTION13chain 'D' and (resid 376 through 434 )
14X-RAY DIFFRACTION14chain 'D' and (resid 435 through 464 )
15X-RAY DIFFRACTION15chain 'D' and (resid 465 through 566 )
16X-RAY DIFFRACTION16chain 'D' and (resid 567 through 580 )
17X-RAY DIFFRACTION17chain 'E' and (resid 376 through 413 )
18X-RAY DIFFRACTION18chain 'E' and (resid 414 through 463 )
19X-RAY DIFFRACTION19chain 'E' and (resid 464 through 579 )
20X-RAY DIFFRACTION20chain 'F' and (resid 376 through 412 )
21X-RAY DIFFRACTION21chain 'F' and (resid 413 through 464 )
22X-RAY DIFFRACTION22chain 'F' and (resid 465 through 511 )
23X-RAY DIFFRACTION23chain 'F' and (resid 512 through 579 )
24X-RAY DIFFRACTION24chain 'G' and (resid 377 through 412 )
25X-RAY DIFFRACTION25chain 'G' and (resid 413 through 464 )
26X-RAY DIFFRACTION26chain 'G' and (resid 465 through 566 )
27X-RAY DIFFRACTION27chain 'G' and (resid 567 through 581 )
28X-RAY DIFFRACTION28chain 'H' and (resid 377 through 412 )
29X-RAY DIFFRACTION29chain 'H' and (resid 413 through 464 )
30X-RAY DIFFRACTION30chain 'H' and (resid 465 through 474 )
31X-RAY DIFFRACTION31chain 'H' and (resid 475 through 579 )

+
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://pdbjlvh1.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