3J3Q

Atomic-level structure of the entire HIV-1 capsid

This is a large structure.

> Summary

Summary for 3J3Q

Related3J34 3J3Y
Integrates1VU4 1VU5 1VU6 1VU7 1VU8 1VU9 1VUA 1VUC 1VUD 1VUE 1VUF 1VUG 1VUH 1VUI 1VUJ 1VUK 1VUL 1VUM 1VUN 1VUO 1VUP 1VUQ 1VUR 1VUS 1VUT
EMDB informationEMD-5639
Descriptorcapsid protein (1 entity in total)
Functional Keywordshiv-1 capsid, core, all-atom model, complete capsid, virus
Biological sourceHuman immunodeficiency virus 1 (HIV-1)
Cellular locationMatrix protein p17: Virion (By similarity). Virion (By similarity) Q79791
Total number of polymer chains1356
Total molecular weight34852576.44
Authors
Perilla, J.R.,Zhao, G.,Zhang, P.,Schulten, K.J. (deposition date: 2013-04-12, release date: 2013-05-29, Last modification date: 2014-12-10)
Primary citation
Zhao, G.,Perilla, J.R.,Yufenyuy, E.L.,Meng, X.,Chen, B.,Ning, J.,Ahn, J.,Gronenborn, A.M.,Schulten, K.,Aiken, C.,Zhang, P.
Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics.
Nature, 497:643-646, 2013
PubMed: 23719463 (PDB entries with the same primary citation)
DOI: 10.1038/nature12162
MImport into Mendeley
Experimental method
ELECTRON MICROSCOPY
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Structure validation

Clashscore0MetricValuePercentile RanksWorseBetterPercentile relative to all structuresPercentile relative to all EM structures

More Asymmetric unit images

Molmil generated image of 3j3q
no rotation
Molmil generated image of 3j3q
rotated about x axis by 90°
Molmil generated image of 3j3q
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
g8, g9, ga, gb, gc...capsid proteinpolymer23125702.51356
UniProt (Q79791)
Pfam (PF00607)
Human immunodeficiency virus 1 (HIV-1)CA

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1356
Total molecular weight34852576.4
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight34852576.4
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:ELECTRON MICROSCOPY

Cell axes1.0001.0001.000
Cell angles90.0090.0090.00
SpacegroupP 1
Resolution limits -
the highest resolution shell value -

Data Collection Statistics

Resolution limits -
the highest resolution shell value -

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
00030430cellular_componenthost cell cytoplasm
00042025cellular_componenthost cell nucleus
00019013cellular_componentviral nucleocapsid
00003723molecular_functionRNA binding
00005198molecular_functionstructural molecule activity
00008270molecular_functionzinc ion binding
00039702biological_processviral budding via host ESCRT complex
00019076biological_processviral release from host cell
10030430cellular_componenthost cell cytoplasm
10042025cellular_componenthost cell nucleus
10019013cellular_componentviral nucleocapsid
10003723molecular_functionRNA binding
10005198molecular_functionstructural molecule activity
10008270molecular_functionzinc ion binding
10039702biological_processviral budding via host ESCRT complex
10019076biological_processviral release from host cell
100030430cellular_componenthost cell cytoplasm
100042025cellular_componenthost cell nucleus
100019013cellular_componentviral nucleocapsid
100003723molecular_functionRNA binding
100005198molecular_functionstructural molecule activity
100008270molecular_functionzinc ion binding
100039702biological_processviral budding via host ESCRT complex
100019076biological_processviral release from host cell
110030430cellular_componenthost cell cytoplasm
110042025cellular_componenthost cell nucleus
110019013cellular_componentviral nucleocapsid
110003723molecular_functionRNA binding
110005198molecular_functionstructural molecule activity
110008270molecular_functionzinc ion binding
110039702biological_processviral budding via host ESCRT complex
110019076biological_processviral release from host cell
120030430cellular_componenthost cell cytoplasm
120042025cellular_componenthost cell nucleus
120019013cellular_componentviral nucleocapsid
120003723molecular_functionRNA binding
120005198molecular_functionstructural molecule activity
120008270molecular_functionzinc ion binding
120039702biological_processviral budding via host ESCRT complex
120019076biological_processviral release from host cell
130030430cellular_componenthost cell cytoplasm
130042025cellular_componenthost cell nucleus
130019013cellular_componentviral nucleocapsid
130003723molecular_functionRNA binding
130005198molecular_functionstructural molecule activity
130008270molecular_functionzinc ion binding
130039702biological_processviral budding via host ESCRT complex
130019076biological_processviral release from host cell
140030430cellular_componenthost cell cytoplasm
140042025cellular_componenthost cell nucleus
140019013cellular_componentviral nucleocapsid
140003723molecular_functionRNA binding
140005198molecular_functionstructural molecule activity
140008270molecular_functionzinc ion binding
140039702biological_processviral budding via host ESCRT complex
140019076biological_processviral release from host cell
150030430cellular_componenthost cell cytoplasm
150042025cellular_componenthost cell nucleus
150019013cellular_componentviral nucleocapsid
150003723molecular_functionRNA binding
150005198molecular_functionstructural molecule activity
150008270molecular_functionzinc ion binding
150039702biological_processviral budding via host ESCRT complex
150019076biological_processviral release from host cell
160030430cellular_componenthost cell cytoplasm
160042025cellular_componenthost cell nucleus
160019013cellular_componentviral nucleocapsid
160003723molecular_functionRNA binding
160005198molecular_functionstructural molecule activity
160008270molecular_functionzinc ion binding
160039702biological_processviral budding via host ESCRT complex
160019076biological_processviral release from host cell
170030430cellular_componenthost cell cytoplasm
170042025cellular_componenthost cell nucleus
170019013cellular_componentviral nucleocapsid
170003723molecular_functionRNA binding
170005198molecular_functionstructural molecule activity
170008270molecular_functionzinc ion binding
170039702biological_processviral budding via host ESCRT complex
170019076biological_processviral release from host cell
180030430cellular_componenthost cell cytoplasm
180042025cellular_componenthost cell nucleus
180019013cellular_componentviral nucleocapsid
180003723molecular_functionRNA binding
180005198molecular_functionstructural molecule activity
180008270molecular_functionzinc ion binding
180039702biological_processviral budding via host ESCRT complex
180019076biological_processviral release from host cell
190030430cellular_componenthost cell cytoplasm
190042025cellular_componenthost cell nucleus
190019013cellular_componentviral nucleocapsid
190003723molecular_functionRNA binding
190005198molecular_functionstructural molecule activity
190008270molecular_functionzinc ion binding
190039702biological_processviral budding via host ESCRT complex
190019076biological_processviral release from host cell
1A0030430cellular_componenthost cell cytoplasm
1A0042025cellular_componenthost cell nucleus
1A0019013cellular_componentviral nucleocapsid
1A0003723molecular_functionRNA binding
1A0005198molecular_functionstructural molecule activity
1A0008270molecular_functionzinc ion binding
1A0039702biological_processviral budding via host ESCRT complex
1A0019076biological_processviral release from host cell
1B0030430cellular_componenthost cell cytoplasm
1B0042025cellular_componenthost cell nucleus
1B0019013cellular_componentviral nucleocapsid
1B0003723molecular_functionRNA binding
1B0005198molecular_functionstructural molecule activity
1B0008270molecular_functionzinc ion binding
1B0039702biological_processviral budding via host ESCRT complex
1B0019076biological_processviral release from host cell
1C0030430cellular_componenthost cell cytoplasm
1C0042025cellular_componenthost cell nucleus
1C0019013cellular_componentviral nucleocapsid
1C0003723molecular_functionRNA binding
1C0005198molecular_functionstructural molecule activity
1C0008270molecular_functionzinc ion binding
1C0039702biological_processviral budding via host ESCRT complex
1C0019076biological_processviral release from host cell
1D0030430cellular_componenthost cell cytoplasm
1D0042025cellular_componenthost cell nucleus
1D0019013cellular_componentviral nucleocapsid
1D0003723molecular_functionRNA binding
1D0005198molecular_functionstructural molecule activity
1D0008270molecular_functionzinc ion binding
1D0039702biological_processviral budding via host ESCRT complex
1D0019076biological_processviral release from host cell
1E0030430cellular_componenthost cell cytoplasm
1E0042025cellular_componenthost cell nucleus
1E0019013cellular_componentviral nucleocapsid
1E0003723molecular_functionRNA binding
1E0005198molecular_functionstructural molecule activity
1E0008270molecular_functionzinc ion binding
1E0039702biological_processviral budding via host ESCRT complex
1E0019076biological_processviral release from host cell
1F0030430cellular_componenthost cell cytoplasm
1F0042025cellular_componenthost cell nucleus
1F0019013cellular_componentviral nucleocapsid
1F0003723molecular_functionRNA binding
1F0005198molecular_functionstructural molecule activity
1F0008270molecular_functionzinc ion binding
1F0039702biological_processviral budding via host ESCRT complex
1F0019076biological_processviral release from host cell
1G0030430cellular_componenthost cell cytoplasm
1G0042025cellular_componenthost cell nucleus
1G0019013cellular_componentviral nucleocapsid
1G0003723molecular_functionRNA binding
1G0005198molecular_functionstructural molecule activity
1G0008270molecular_functionzinc ion binding
1G0039702biological_processviral budding via host ESCRT complex
1G0019076biological_processviral release from host cell
1H0030430cellular_componenthost cell cytoplasm
1H0042025cellular_componenthost cell nucleus
1H0019013cellular_componentviral nucleocapsid
1H0003723molecular_functionRNA binding
1H0005198molecular_functionstructural molecule activity
1H0008270molecular_functionzinc ion binding
1H0039702biological_processviral budding via host ESCRT complex
1H0019076biological_processviral release from host cell
1I0030430cellular_componenthost cell cytoplasm
1I0042025cellular_componenthost cell nucleus
1I0019013cellular_componentviral nucleocapsid
1I0003723molecular_functionRNA binding
1I0005198molecular_functionstructural molecule activity
1I0008270molecular_functionzinc ion binding
1I0039702biological_processviral budding via host ESCRT complex
1I0019076biological_processviral release from host cell
1J0030430cellular_componenthost cell cytoplasm
1J0042025cellular_componenthost cell nucleus
1J0019013cellular_componentviral nucleocapsid
1J0003723molecular_functionRNA binding
1J0005198molecular_functionstructural molecule activity
1J0008270molecular_functionzinc ion binding
1J0039702biological_processviral budding via host ESCRT complex
1J0019076biological_processviral release from host cell
1K0030430cellular_componenthost cell cytoplasm
1K0042025cellular_componenthost cell nucleus
1K0019013cellular_componentviral nucleocapsid
1K0003723molecular_functionRNA binding
1K0005198molecular_functionstructural molecule activity
1K0008270molecular_functionzinc ion binding
1K0039702biological_processviral budding via host ESCRT complex
1K0019076biological_processviral release from host cell
1L0030430cellular_componenthost cell cytoplasm
1L0042025cellular_componenthost cell nucleus
1L0019013cellular_componentviral nucleocapsid
1L0003723molecular_functionRNA binding
1L0005198molecular_functionstructural molecule activity
1L0008270molecular_functionzinc ion binding
1L0039702biological_processviral budding via host ESCRT complex
1L0019076biological_processviral release from host cell
1M0030430cellular_componenthost cell cytoplasm
1M0042025cellular_componenthost cell nucleus
1M0019013cellular_componentviral nucleocapsid
1M0003723molecular_functionRNA binding
1M0005198molecular_functionstructural molecule activity
1M0008270molecular_functionzinc ion binding
1M0039702biological_processviral budding via host ESCRT complex
1M0019076biological_processviral release from host cell
1N0030430cellular_componenthost cell cytoplasm
1N0042025cellular_componenthost cell nucleus
1N0019013cellular_componentviral nucleocapsid
1N0003723molecular_functionRNA binding
1N0005198molecular_functionstructural molecule activity
1N0008270molecular_functionzinc ion binding
1N0039702biological_processviral budding via host ESCRT complex
1N0019076biological_processviral release from host cell
1O0030430cellular_componenthost cell cytoplasm
1O0042025cellular_componenthost cell nucleus
1O0019013cellular_componentviral nucleocapsid
1O0003723molecular_functionRNA binding
1O0005198molecular_functionstructural molecule activity
1O0008270molecular_functionzinc ion binding
1O0039702biological_processviral budding via host ESCRT complex
1O0019076biological_processviral release from host cell
1P0030430cellular_componenthost cell cytoplasm
1P0042025cellular_componenthost cell nucleus
1P0019013cellular_componentviral nucleocapsid
1P0003723molecular_functionRNA binding
1P0005198molecular_functionstructural molecule activity
1P0008270molecular_functionzinc ion binding
1P0039702biological_processviral budding via host ESCRT complex
1P0019076biological_processviral release from host cell
1Q0030430cellular_componenthost cell cytoplasm
1Q0042025cellular_componenthost cell nucleus
1Q0019013cellular_componentviral nucleocapsid
1Q0003723molecular_functionRNA binding
1Q0005198molecular_functionstructural molecule activity
1Q0008270molecular_functionzinc ion binding
1Q0039702biological_processviral budding via host ESCRT complex
1Q0019076biological_processviral release from host cell
1R0030430cellular_componenthost cell cytoplasm
1R0042025cellular_componenthost cell nucleus
1R0019013cellular_componentviral nucleocapsid
1R0003723molecular_functionRNA binding
1R0005198molecular_functionstructural molecule activity
1R0008270molecular_functionzinc ion binding
1R0039702biological_processviral budding via host ESCRT complex
1R0019076biological_processviral release from host cell
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

Sequence navigator - 3j3q: Chain g8,g9,ga,gb,gc,gd,ge,gf,gg,gh,1C,gi,gj,gk,gl,gm,gn,go,gp,gq,gr,1D,gs,gt,gu,gv,gw,gx,gy,gz,gA,gB,1E,gC,gD,gE,gF,gG,gH,gI,gJ,gK,gL,1F,gM,gN,gO,gP,gQ,gR,gS,gT,gU,gV,1G,gW,gX,gY,gZ,h0,h1,h2,h3,h4,h5,1H,h6,h7,h8,h9,ha,hb,hc,hd,he,hf,1I,hg,hh,hi,hj,hk,hl,hm,hn,ho,hp,1J,hq,hr,hs,ht,hu,hv,hw,hx,hy,hz,1K,hA,hB,hC,hD,hE,hF,hG,hH,hI,hJ,1L,hK,hL,hM,hN,hO,hP,hQ,hR,hS,hT,1M,hU,hV,hW,hX,hY,hZ,i0,i1,i2,i3,1N,i4,i5,i6,i7,i8,i9,ia,ib,ic,id,1O,ie,if,ig,ih,ii,ij,ik,il,im,in,1P,io,ip,iq,ir,is,it,iu,iv,iw,ix,1Q,iy,iz,iA,iB,iC,iD,iE,iF,iG,iH,1R,iI,iJ,iK,iL,iM,iN,iO,iP,iQ,iR,1S,iS,iT,iU,iV,iW,iX,iY,iZ,j0,j1,1T,j2,j3,j4,j5,j6,j7,j8,j9,ja,jb,1U,jc,jd,je,jf,jg,jh,ji,jj,jk,jl,1V,jm,jn,jo,jp,jq,jr,js,jt,ju,jv,1W,jw,jx,jy,jz,jA,jB,jC,jD,jE,jF,1X,jG,jH,jI,jJ,jK,jL,jM,jN,jO,jP,1Y,jQ,jR,jS,jT,jU,jV,jW,jX,jY,jZ,1Z,k0,k1,k2,k3,k4,k5,k6,k7,k8,k9,20,ka,kb,kc,kd,ke,kf,kg,kh,ki,kj,21,kk,kl,km,kn,ko,kp,kq,kr,ks,kt,22,ku,kv,kw,kx,ky,kz,kA,kB,kC,kD,23,kE,kF,kG,kH,kI,kJ,kK,kL,kM,kN,24,kO,kP,kQ,kR,kS,kT,kU,kV,kW,kX,25,kY,kZ,l0,l1,l2,l3,l4,l5,l6,l7,26,l8,l9,la,lb,lc,ld,le,lf,lg,lh,27,li,lj,lk,ll,lm,ln,lo,lp,lq,lr,28,ls,lt,lu,lv,lw,lx,ly,lz,lA,lB,29,lC,lD,lE,lF,lG,lH,lI,lJ,lK,lL,2a,lM,lN,lO,lP,lQ,lR,2b,2c,2d,2e,2f,2g,2h,2i,2j,2k,2l,2m,2n,2o,2p,2q,2r,2s,2t,2u,2v,2w,2x,2y,2z,2A,2B,2C,2D,2E,2F,2G,2H,2I,2J,2K,2L,2M,2N,2O,2P,2Q,2R,2S,2T,2U,2V,2W,2X,2Y,2Z,30,31,32,33,34,35,36,37,38,39,3a,3b,3c,3d,3e,3f,3g,3h,3i,3j,3k,3l,3m,3n,3o,3p,3q,3r,3s,3t,3u,3v,3w,3x,3y,3z,3A,3B,3C,3D,3E,3F,3G,3H,3I,3J,3K,3L,3M,3N,3O,3P,3Q,3R,3S,3T,3U,3V,3W,3X,3Y,3Z,40,41,42,43,44,45,46,47,48,49,4a,4b,4c,4d,4e,4f,4g,4h,4i,4j,4k,4l,4m,4n,4o,4p,4q,4r,4s,4t,4u,4v,4w,4x,4y,4z,4A,4B,4C,4D,4E,4F,4G,4H,4I,4J,4K,4L,4M,4N,4O,4P,4Q,4R,4S,4T,4U,4V,4W,4X,4Y,4Z,50,51,52,53,54,55,56,57,58,59,5a,5b,5c,5d,5e,5f,5g,5h,5i,5j,5k,5l,5m,5n,5o,5p,5q,5r,5s,5t,5u,5v,5w,5x,5y,5z,5A,5B,5C,5D,5E,5F,5G,5H,5I,5J,5K,5L,5M,5N,5O,5P,5Q,5R,5S,5T,5U,5V,5W,5X,5Y,5Z,60,61,62,63,64,65,66,67,68,69,6a,6b,6c,6d,6e,6f,6g,6h,6i,6j,6k,6l,6m,6n,6o,6p,6q,6r,6s,6t,6u,6v,6w,6x,6y,6z,6A,6B,6C,6D,6E,6F,6G,6H,6I,6J,6K,6L,6M,6N,6O,6P,6Q,6R,6S,6T,6U,6V,6W,6X,6Y,6Z,70,71,72,73,74,75,76,77,78,79,7a,7b,7c,7d,7e,7f,7g,7h,7i,7j,7k,7l,7m,7n,7o,7p,7q,7r,7s,7t,7u,7v,7w,7x,7y,7z,7A,7B,7C,7D,7E,7F,7G,7H,7I,7J,7K,7L,7M,7N,7O,7P,7Q,7R,7S,7T,7U,7V,7W,7X,7Y,7Z,80,81,82,83,84,85,86,87,88,89,8a,8b,8c,8d,8e,8f,8g,8h,8i,8j,8k,8l,8m,8n,8o,8p,8q,8r,8s,8t,8u,8v,8w,8x,8y,8z,8A,8B,8C,8D,8E,8F,8G,8H,8I,8J,8K,8L,8M,8N,8O,8P,8Q,8R,8S,8T,8U,8V,8W,8X,8Y,8Z,90,91,92,93,94,95,96,97,98,99,9a,9b,9c,9d,9e,9f,9g,9h,9i,9j,9k,9l,9m,9n,9o,9p,9q,9r,9s,9t,9u,9v,9w,9x,9y,9z,9A,9B,9C,9D,9E,9F,9G,9H,9I,9J,9K,9L,9M,9N,9O,9P,Y,9Q,9R,9S,9T,9U,9V,9W,9X,9Y,9Z,Z,a0,a1,a2,a3,a4,a5,a6,a7,a8,a9,10,aa,ab,ac,ad,ae,af,ag,ah,ai,aj,11,ak,al,am,an,ao,ap,aq,ar,as,at,12,au,av,aw,ax,ay,az,aA,aB,aC,aD,13,aE,aF,aG,aH,aI,aJ,aK,aL,aM,aN,14,aO,aP,aQ,aR,aS,aT,aU,aV,aW,aX,15,aY,aZ,b0,b1,b2,b3,b4,b5,b6,b7,16,b8,b9,ba,bb,bc,bd,be,bf,bg,bh,17,bi,bj,bk,bl,bm,bn,bo,bp,bq,br,18,bs,bt,bu,bv,bw,bx,by,bz,bA,bB,19,bC,bD,bE,bF,bG,bH,bI,bJ,bK,bL,1a,bM,bN,bO,bP,bQ,bR,bS,bT,bU,bV,1b,bW,bX,bY,bZ,c0,c1,c2,c3,c4,c5,1c,c6,c7,c8,c9,ca,cb,cc,cd,ce,cf,1d,cg,ch,ci,cj,ck,cl,cm,cn,co,cp,1e,cq,cr,cs,ct,cu,cv,cw,cx,cy,cz,1f,cA,cB,cC,cD,cE,cF,cG,cH,cI,cJ,1g,cK,cL,cM,cN,cO,cP,cQ,cR,cS,cT,1h,cU,cV,cW,cX,cY,cZ,d0,d1,d2,d3,1i,d4,d5,d6,d7,d8,d9,da,db,dc,dd,1j,de,df,dg,dh,di,dj,dk,dl,dm,dn,1k,do,dp,dq,dr,ds,dt,du,dv,dw,dx,1l,dy,dz,dA,dB,dC,dD,dE,dF,dG,dH,1m,dI,dJ,dK,dL,dM,dN,dO,dP,dQ,dR,1n,dS,dT,dU,dV,dW,dX,dY,dZ,e0,e1,1o,e2,e3,e4,e5,e6,e7,e8,e9,ea,eb,1p,ec,ed,ee,ef,eg,eh,ei,ej,ek,el,1q,em,en,eo,ep,eq,er,es,et,eu,ev,1r,ew,ex,ey,ez,eA,eB,eC,eD,eE,eF,1s,eG,eH,eI,eJ,eK,eL,eM,eN,eO,eP,1t,eQ,eR,eS,eT,eU,eV,eW,eX,eY,eZ,1u,f0,f1,f2,f3,f4,f5,f6,f7,f8,f9,1v,fa,fb,fc,fd,fe,ff,fg,fh,fi,fj,1w,fk,fl,fm,fn,fo,fp,fq,fr,fs,ft,1x,fu,fv,fw,fx,fy,fz,fA,fB,fC,fD,1y,fE,fF,fG,fH,fI,fJ,fK,fL,fM,fN,1z,fO,fP,fQ,fR,fS,fT,fU,fV,fW,fX,1A,fY,fZ,g0,g1,g2,g3,g4,g5,g6,g7,1B,0,a,b,c,d,e,f,g,h,i,j,1,k,l,m,n,o,p,q,r,s,t,2,u,v,w,x,y,z,A,B,C,D,3,E,F,G,H,I,J,K,L,M,N,4,O,P,Q,R,S,T,U,V,W,X,5,6,7,8,9

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