7NDG
Cryo-em structure of the ternary complex between netrin-1, neogenin and repulsive guidance molecule b
PDB DOI: 10.2210/pdb7ndg/pdb
Classification: SIGNALING PROTEIN Organism(s): Homo Sapiens , Mus Musculus
Deposited: 2021-02-01 Deposition Author(s): Aricescu, A.R. , Bishop, B. , Brignani, S. , De Ruiter, A.A. , Dudukcu, O. , Elegheert, J. , Griffiths, S.C. , Karia, D. , Malinauskaite, L. , Malinauskas, T. , Pasterkamp, R.J. , Robinson, R.A. , Schwab, R.A. , Siebold, C. , Van Battum, E.Y. , Van De Haar, L.L. , Van Den Heuvel, D.M.A. , Van Den Munkhof, M. , Zelina, P.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 5.98 Å
Cryo-em structure of the ternary complex between netrin-1, neogenin and repulsive guidance molecule b
Aricescu, A.R. , Bishop, B. , Brignani, S. , De Ruiter, A.A. , Dudukcu, O. , Elegheert, J. , Griffiths, S.C. , Karia, D. , Malinauskaite, L. , Malinauskas, T. , Pasterkamp, R.J. , Robinson, R.A. , Schwab, R.A. , Siebold, C. , Van Battum, E.Y. , Van De Haar, L.L. , Van Den Heuvel, D.M.A. , Van Den Munkhof, M. , Zelina, P.
Primary Citation of Related Structures: 7NDG
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| Netrin-1 | A | 441 | Homo Sapiens , Mus Musculus | GPGLSMFAGQAAQPDPCSDENGHPRRCIPDFVNAAFGKDVRVSSTCGRPPARYCVVSERGEERLRSCHLCNASDPKKAHPPAFLTDLNNPHNLTCWQSENYLQFPHNVTLTLSLGKKFEVTYVSLQFCSPRPESMAIYKSMDYGRTWVPFQFYSTQCRKMYNRPHRAPITKQNEQEAVCTDSHTDMRPLSGGLIAFSTLDGRPSAHDFDNSPVLQDWVTATDIRVAFSRLHTFGDENEDDSELARDSYFYAVSDLQVGGRCKCNGHAARCVRDRDDSLVCDCRHNTAGPECDRCKPFHYDRPWQRATAREANECVACNCNLHARRCRFNMELYKLSGRKSGGVCLNCRHNTAGRHCHYCKEGYYRDMGKPITHRKACKACDCHPVGAAGKTCNQTTGQCPCKDGVTGITCNRCAKGYQQSRSPIAPCIKGSGTETSQVAPA |
| Netrin-1 | G | 441 | Homo Sapiens , Mus Musculus | GPGLSMFAGQAAQPDPCSDENGHPRRCIPDFVNAAFGKDVRVSSTCGRPPARYCVVSERGEERLRSCHLCNASDPKKAHPPAFLTDLNNPHNLTCWQSENYLQFPHNVTLTLSLGKKFEVTYVSLQFCSPRPESMAIYKSMDYGRTWVPFQFYSTQCRKMYNRPHRAPITKQNEQEAVCTDSHTDMRPLSGGLIAFSTLDGRPSAHDFDNSPVLQDWVTATDIRVAFSRLHTFGDENEDDSELARDSYFYAVSDLQVGGRCKCNGHAARCVRDRDDSLVCDCRHNTAGPECDRCKPFHYDRPWQRATAREANECVACNCNLHARRCRFNMELYKLSGRKSGGVCLNCRHNTAGRHCHYCKEGYYRDMGKPITHRKACKACDCHPVGAAGKTCNQTTGQCPCKDGVTGITCNRCAKGYQQSRSPIAPCIKGSGTETSQVAPA |
| Netrin-1 | D | 441 | Homo Sapiens , Mus Musculus | GPGLSMFAGQAAQPDPCSDENGHPRRCIPDFVNAAFGKDVRVSSTCGRPPARYCVVSERGEERLRSCHLCNASDPKKAHPPAFLTDLNNPHNLTCWQSENYLQFPHNVTLTLSLGKKFEVTYVSLQFCSPRPESMAIYKSMDYGRTWVPFQFYSTQCRKMYNRPHRAPITKQNEQEAVCTDSHTDMRPLSGGLIAFSTLDGRPSAHDFDNSPVLQDWVTATDIRVAFSRLHTFGDENEDDSELARDSYFYAVSDLQVGGRCKCNGHAARCVRDRDDSLVCDCRHNTAGPECDRCKPFHYDRPWQRATAREANECVACNCNLHARRCRFNMELYKLSGRKSGGVCLNCRHNTAGRHCHYCKEGYYRDMGKPITHRKACKACDCHPVGAAGKTCNQTTGQCPCKDGVTGITCNRCAKGYQQSRSPIAPCIKGSGTETSQVAPA |
| Neogenin | B | 354 | Homo Sapiens , Mus Musculus | ETGETRVPEVPSSLHVRPLVTSIVVSWTPPENQNIVVRGYAIGYGIGSPHAQTIKVDYKQRYYTIENLDPSSHYVITLKAFNNVGEGIPLYESAVTRPHTVPDPTPMMPPVGVQASILSHDTIRITWADNSLPKHQKITDSRYYTVRWKTNIPANTKYKNANATTLSYLVTGLKPNTLYEFSVMVTKGRRSSTWSMTAHGATFELVPTSPPKDVTVVSKEGKPRTIIVNWQPPSEANGKITGYIIYYSTDVNAEIHDWVIEPVVGNRLTHQIQELTLDTPYYFKIQARNSKGMGPMSEAVQFRTPKALGSAGKGSRLPDLGSDYKPPMSGSNSPHGSPTSPLDSNGTKHHHHHH |
| Neogenin | H | 354 | Homo Sapiens , Mus Musculus | ETGETRVPEVPSSLHVRPLVTSIVVSWTPPENQNIVVRGYAIGYGIGSPHAQTIKVDYKQRYYTIENLDPSSHYVITLKAFNNVGEGIPLYESAVTRPHTVPDPTPMMPPVGVQASILSHDTIRITWADNSLPKHQKITDSRYYTVRWKTNIPANTKYKNANATTLSYLVTGLKPNTLYEFSVMVTKGRRSSTWSMTAHGATFELVPTSPPKDVTVVSKEGKPRTIIVNWQPPSEANGKITGYIIYYSTDVNAEIHDWVIEPVVGNRLTHQIQELTLDTPYYFKIQARNSKGMGPMSEAVQFRTPKALGSAGKGSRLPDLGSDYKPPMSGSNSPHGSPTSPLDSNGTKHHHHHH |
| Neogenin | E | 354 | Homo Sapiens , Mus Musculus | ETGETRVPEVPSSLHVRPLVTSIVVSWTPPENQNIVVRGYAIGYGIGSPHAQTIKVDYKQRYYTIENLDPSSHYVITLKAFNNVGEGIPLYESAVTRPHTVPDPTPMMPPVGVQASILSHDTIRITWADNSLPKHQKITDSRYYTVRWKTNIPANTKYKNANATTLSYLVTGLKPNTLYEFSVMVTKGRRSSTWSMTAHGATFELVPTSPPKDVTVVSKEGKPRTIIVNWQPPSEANGKITGYIIYYSTDVNAEIHDWVIEPVVGNRLTHQIQELTLDTPYYFKIQARNSKGMGPMSEAVQFRTPKALGSAGKGSRLPDLGSDYKPPMSGSNSPHGSPTSPLDSNGTKHHHHHH |
| Repulsive Guidance Molecule B (C-terminal region) | F | 252 | Homo Sapiens , Mus Musculus | PHLRTFKDNFQTCKVEGAWPLIDNNYLSVQVTNVPVVPGSSATATNKITIIFKAHHECTDQKVYQAVTDDLPAAFVDGTTSGGDSDAKSLRIVERESGHYVEMHARYIGTTVFVRQVGRYLTLAIRMPEDLAMSYEESQDLQLCVNGCPLSERIDDGQGQVSAILGHSLPRTSLVQAWPGYTLETANTQCHEKMPVKDIYFQSCVFDLLTTGDANFTAAAHSALEDVEALHPRKERWHIFPSSGTKHHHHHH |
| Repulsive Guidance Molecule B (C-terminal region) | C | 252 | Homo Sapiens , Mus Musculus | PHLRTFKDNFQTCKVEGAWPLIDNNYLSVQVTNVPVVPGSSATATNKITIIFKAHHECTDQKVYQAVTDDLPAAFVDGTTSGGDSDAKSLRIVERESGHYVEMHARYIGTTVFVRQVGRYLTLAIRMPEDLAMSYEESQDLQLCVNGCPLSERIDDGQGQVSAILGHSLPRTSLVQAWPGYTLETANTQCHEKMPVKDIYFQSCVFDLLTTGDANFTAAAHSALEDVEALHPRKERWHIFPSSGTKHHHHHH |
| Repulsive Guidance Molecule B (C-terminal region) | I | 252 | Homo Sapiens , Mus Musculus | PHLRTFKDNFQTCKVEGAWPLIDNNYLSVQVTNVPVVPGSSATATNKITIIFKAHHECTDQKVYQAVTDDLPAAFVDGTTSGGDSDAKSLRIVERESGHYVEMHARYIGTTVFVRQVGRYLTLAIRMPEDLAMSYEESQDLQLCVNGCPLSERIDDGQGQVSAILGHSLPRTSLVQAWPGYTLETANTQCHEKMPVKDIYFQSCVFDLLTTGDANFTAAAHSALEDVEALHPRKERWHIFPSSGTKHHHHHH |
| RGM domain family member B | N | 119 | Homo Sapiens , Mus Musculus | ETGQCRIQKCTTDFVSLTSHLNSAVDGFDSEFCKALRAYAGCTQRTSKACRGNLVYHSAVLGISDLMSQRNCSKDGPTSSTNPEVTHDPCNYHSHAGAREHRRGDQNPPSYLFCGLFGD |
| RGM domain family member B | M | 119 | Homo Sapiens , Mus Musculus | ETGQCRIQKCTTDFVSLTSHLNSAVDGFDSEFCKALRAYAGCTQRTSKACRGNLVYHSAVLGISDLMSQRNCSKDGPTSSTNPEVTHDPCNYHSHAGAREHRRGDQNPPSYLFCGLFGD |
| RGM domain family member B | O | 119 | Homo Sapiens , Mus Musculus | ETGQCRIQKCTTDFVSLTSHLNSAVDGFDSEFCKALRAYAGCTQRTSKACRGNLVYHSAVLGISDLMSQRNCSKDGPTSSTNPEVTHDPCNYHSHAGAREHRRGDQNPPSYLFCGLFGD |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2021-02-01 Deposition Author(s): Aricescu, A.R. , Bishop, B. , Brignani, S. , De Ruiter, A.A. , Dudukcu, O. , Elegheert, J. , Griffiths, S.C. , Karia, D. , Malinauskaite, L. , Malinauskas, T. , Pasterkamp, R.J. , Robinson, R.A. , Schwab, R.A. , Siebold, C. , Van Battum, E.Y. , Van De Haar, L.L. , Van Den Heuvel, D.M.A. , Van Den Munkhof, M. , Zelina, P.