Structure of VRC44.01 Fab in complex with 3BNC117-purified C1080.c3 RnS SOSIP.664 HIV-1 Env trimer
Resolution: 2.83 Å
EM Method: Single-particle
Fitted PDBs: 9bio
Q-score: 0.547
Cale EM, Shen CH, Olia AS, Radakovich NA, Rawi R, Yang Y, Ambrozak DR, Bennici AK, Chuang GY, Crooks ED, Driscoll JI, Lin BC, Louder MK, Madden PJ, Messina MA, Osawa K, Stewart-Jones GBE, Verardi R, Vrakas Z, Xie D, Zhang B, Binley JM, Connors M, Koup RA, Pierson TC, Doria-Rose NA, Kwong PD, Mascola JR, Gorman J
Cell Rep (2024) 43 pp. 115010-115010 [ Pubmed: 39675002 DOI: doi:10.1016/j.celrep.2024.115010 ]
- 3bnc117 light chain (23 kDa, Protein from Homo sapiens)
- Phosphate ion (94 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- 3bnc117 heavy chain (24 kDa, Protein from Homo sapiens)
- Vrc44.01 heavy chain (13 kDa, Protein from Homo sapiens)
- Envelope glycoprotein gp160 (54 kDa, Protein from Human immunodeficiency virus 1)
- Vrc44 and 3bnc117 fabs with repaired c1080 env trimer (Complex from Human immunodeficiency virus 1)
- Vrc44.01 light chain (11 kDa, Protein from Homo sapiens)
- Envelope glycoprotein gp41 (19 kDa, Protein from Human immunodeficiency virus 1)
a peptide receptor complex structure
Resolution: 2.68 Å
EM Method: Single-particle
Fitted PDBs: 8xgo
Q-score: 0.535
Wu Z, Chen G, Qiu C, Yan X, Xu L, Jiang S, Xu J, Han R, Shi T, Liu Y, Gao W, Wang Q, Li J, Ye F, Pan X, Zhang Z, Ning P, Zhang B, Chen J, Du Y
Sci Adv (2024) 10 pp. eadn7771-eadn7771 [ Pubmed: 39151001 DOI: doi:10.1126/sciadv.adn7771 ]
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Kiss1r (Complex)
- Scfv16 (Complex)
- Kissar-gq-scfv16 (130 kDa, Complex from Homo sapiens)
- Kiss1r,guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1,guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2,guanine nucleotide-binding protein g(q) subunit alpha (Complex)
- Kiss-1 receptor (42 kDa, Protein from Homo sapiens)
- Tak448 (1 kDa, Protein from synthetic construct)
- Guanine nucleotide-binding protein g(q) subunit alpha (41 kDa, Protein from Homo sapiens)
- Scfv16 (27 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Homo sapiens)
a peptide receptor complex structure
Resolution: 2.95 Å
EM Method: Single-particle
Fitted PDBs: 8xgs
Q-score: 0.475
Wu Z, Chen G, Qiu C, Yan X, Xu L, Jiang S, Xu J, Han R, Shi T, Liu Y, Gao W, Wang Q, Li J, Ye F, Pan X, Zhang Z, Ning P, Zhang B, Chen J, Du Y
Sci Adv (2024) 10 pp. eadn7771-eadn7771 [ Pubmed: 39151001 DOI: doi:10.1126/sciadv.adn7771 ]
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Scfv16 (Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1,guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2,guanine nucleotide-binding protein g(q) subunit alpha (Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(q) subunit alpha (41 kDa, Protein from Homo sapiens)
- Kiss1r (Complex from Homo sapiens)
- Metastin (5 kDa, Protein from synthetic construct)
- Kiss-1 receptor (42 kDa, Protein from Homo sapiens)
- Kp54-kiss1r-gq-scfv16 (130 kDa, Complex from Homo sapiens)
- Scfv16 (27 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Homo sapiens)
a peptide receptor complex structure
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8xgu
Q-score: 0.482
Wu Z, Chen G, Qiu C, Yan X, Xu L, Jiang S, Xu J, Han R, Shi T, Liu Y, Gao W, Wang Q, Li J, Ye F, Pan X, Zhang Z, Ning P, Zhang B, Chen J, Du Y
Sci Adv (2024) 10 pp. eadn7771-eadn7771 [ Pubmed: 39151001 DOI: doi:10.1126/sciadv.adn7771 ]
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Homo sapiens)
- Scfv16 (Complex from Homo sapiens)
- Kiss1r (Complex from Homo sapiens)
- Kiss-1 receptor (42 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
- Tak448 (1 kDa, Protein from synthetic construct)
- Kp54-kiss1r-gq-scfv16 (130 kDa, Complex from Homo sapiens)
- Scfv16 (27 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1,guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2,guanine nucleotide-binding protein g(i) subunit alpha-1 (Complex from Homo sapiens)
Cryo-EM structure of Mycobacterium tuberculosis DppABCD in apo form
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 8wd9
Q-score: 0.528
To Be Published
- Probable periplasmic dipeptide-binding lipoprotein dppa (56 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Probable dipeptide-transport integral membrane protein abc transporter dppb (32 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Palmitic acid (256 Da, Ligand)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Probable dipeptide-transport integral membrane protein abc transporter dppc (30 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Dppabcd (Complex from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Probable dipeptide-transport atp-binding protein abc transporter dppd (59 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Cryo-EM structure of the substrate-bound DppABCD complex
Resolution: 3.26 Å
EM Method: Single-particle
Fitted PDBs: 8wda
Q-score: 0.545
To Be Published
- Probable periplasmic dipeptide-binding lipoprotein dppa (56 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Probable dipeptide-transport integral membrane protein abc transporter dppb (32 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Palmitic acid (256 Da, Ligand)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Probable dipeptide-transport integral membrane protein abc transporter dppc (30 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Dppabcd (Complex from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Probable dipeptide-transport atp-binding protein abc transporter dppd (59 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Tetrapeptide (330 Da, Protein from Mycolicibacterium smegmatis MC2 155)
Cryo-EM structure of the ATP-bound DppABCD complex
Resolution: 2.86 Å
EM Method: Single-particle
Fitted PDBs: 8wdb
Q-score: 0.605
To Be Published
- Probable periplasmic dipeptide-binding lipoprotein dppa (56 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Probable dipeptide-transport integral membrane protein abc transporter dppb (32 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Probable dipeptide-transport atp-binding protein abc transporter dppd (59 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Probable dipeptide-transport integral membrane protein abc transporter dppc (30 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Dppabcd (Complex from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
Cryo-EM structure of the ATP-bound Mtb DppABCD with the D445A mutation of DppA
Resolution: 3.89 Å
EM Method: Single-particle
Fitted PDBs: 8xfc
Q-score: 0.425
To Be Published
- Probable dipeptide-transport integral membrane protein abc transporter dppb (32 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Probable dipeptide-transport atp-binding protein abc transporter dppd (59 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Dppabcd (Complex from Mycobacterium tuberculosis H37Rv)
- Probable dipeptide-transport integral membrane protein abc transporter dppc (30 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Probable periplasmic dipeptide-binding lipoprotein dppa (56 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Adenosine-5'-triphosphate (507 Da, Ligand)
CRYO-EM STRUCTURE OF HIV-1 BG505DS-SOSIP.664 ENV TRIMER BOUND TO DJ85-b.01 FAB
Wang H, Cheng C, Dal Santo JL, Shen CH, Bylund T, Henry AR, Howe CA, Hwang J, Morano NC, Morris DJ, Pletnev S, Roark RS, Zhou T, Hansen BT, Hoyt FH, Johnston TS, Wang S, Zhang B, Ambrozak DR, Becker JE, Bender MF, Changela A, Chaudhary R, Corcoran M, Corrigan AR, Foulds KE, Guo Y, Lee M, Li Y, Lin BC, Liu T, Louder MK, Mandolesi M, Mason RD, McKee K, Nair V, O'Dell S, Olia AS, Ou L, Pegu A, Raju N, Rawi R, Roberts-Torres J, Sarfo EK, Sastry M, Schaub AJ, Schmidt SD, Schramm CA, Schwartz CL, Smith SC, Stephens T, Stuckey J, Teng IT, Todd JP, Tsybovsky Y, Van Wazer DJ, Wang S, Doria-Rose NA, Fischer ER, Georgiev IS, Karlsson Hedestam GB, Sheng Z, Woodward RA, Douek DC, Koup RA, Pierson TC, Shapiro L, Shaw GM, Mascola JR, Kwong PD
Cell (2024) 187 pp. 7214-7231.e23 [ Pubmed: 39471811 DOI: doi:10.1016/j.cell.2024.10.003 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Dj85-b.01 fab (Complex from Homo sapiens)
- Bg505 ds-sosip surface protein gp120 (54 kDa, Protein from Human immunodeficiency virus 1)
- Bg505 ds-sosip transmembrane protein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Bg505 ds-sosip dj85-b.01 fab complex (Complex)
- Bg505 ds-sosip (Complex from Human immunodeficiency virus 1)
- Dj85-b.01 fab light chain (23 kDa, Protein from Homo sapiens)
- Dj85-b.01 fab heavy chain (25 kDa, Protein from Homo sapiens)
CRYO-EM STRUCTURE OF HIV-1 BG505DS-SOSIP.664 ENV TRIMER BOUND TO DJ85-c.01 FAB
Wang H, Cheng C, Dal Santo JL, Shen CH, Bylund T, Henry AR, Howe CA, Hwang J, Morano NC, Morris DJ, Pletnev S, Roark RS, Zhou T, Hansen BT, Hoyt FH, Johnston TS, Wang S, Zhang B, Ambrozak DR, Becker JE, Bender MF, Changela A, Chaudhary R, Corcoran M, Corrigan AR, Foulds KE, Guo Y, Lee M, Li Y, Lin BC, Liu T, Louder MK, Mandolesi M, Mason RD, McKee K, Nair V, O'Dell S, Olia AS, Ou L, Pegu A, Raju N, Rawi R, Roberts-Torres J, Sarfo EK, Sastry M, Schaub AJ, Schmidt SD, Schramm CA, Schwartz CL, Smith SC, Stephens T, Stuckey J, Teng IT, Todd JP, Tsybovsky Y, Van Wazer DJ, Wang S, Doria-Rose NA, Fischer ER, Georgiev IS, Karlsson Hedestam GB, Sheng Z, Woodward RA, Douek DC, Koup RA, Pierson TC, Shapiro L, Shaw GM, Mascola JR, Kwong PD
Cell (2024) 187 pp. 7214-7231.e23 [ Pubmed: 39471811 DOI: doi:10.1016/j.cell.2024.10.003 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Dj85-c.01 fab light chain (23 kDa, Protein from Homo sapiens)
- Bg505 ds-sosip surface protein gp120 (54 kDa, Protein from Human immunodeficiency virus 1)
- Dj85-c.01 fab heavy chain (25 kDa, Protein from Homo sapiens)
- Bg505 ds-sosip transmembrane protein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Bg505 ds-sosip (Complex from Human immunodeficiency virus 1)
- Bg505 ds-sosip dj85-c.01 fab complex (Complex)
- Dj85-c.01 fab (Complex from Homo sapiens)