7Y4P
 
 | | Human Plexin A1, extracellular domains 1-4 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Plexin-A1 | | Authors: | Tanaka, T, Neyazaki, M, Nogi, T. | | Deposit date: | 2022-06-15 | | Release date: | 2022-10-19 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (3.5 Å) | | Cite: | Hybrid in vitro/in silico analysis of low-affinity protein-protein interactions that regulate signal transduction by Sema6D.
Protein Sci., 31, 2022
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7Y4O
 | | Rat Semaphorin 6D extracellular region | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Semaphorin 6D | | Authors: | Tanaka, T, Neyazaki, M, Nogi, T. | | Deposit date: | 2022-06-15 | | Release date: | 2022-10-19 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Hybrid in vitro/in silico analysis of low-affinity protein-protein interactions that regulate signal transduction by Sema6D.
Protein Sci., 31, 2022
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6AL1
 | | The NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicus S2P homolog with the PA12 tag inserted between the residues 181 and 184 | | Descriptor: | Heavy chain of antigen binding fragment, Fab of NZ-1, Light chain of antigen binding fragment, ... | | Authors: | Tamura, R, Oi, R, Kaneko, M.K, Kato, Y, Nogi, T. | | Deposit date: | 2018-09-05 | | Release date: | 2019-02-13 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Application of the NZ-1 Fab as a crystallization chaperone for PA tag-inserted target proteins.
Protein Sci., 28, 2019
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6AKQ
 | | The PDZ tandem fragment of A. aeolicus S2P homolog with the PA12 tag inserted between the residues 263 and 267 | | Descriptor: | PDZ tandem fragment of A. aeolicus site-2 protease homolog with the PA tag insertion | | Authors: | Tamura, R, Oi, R, Kaneko, M.K, Kato, Y, Nogi, T. | | Deposit date: | 2018-09-03 | | Release date: | 2019-02-13 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Application of the NZ-1 Fab as a crystallization chaperone for PA tag-inserted target proteins.
Protein Sci., 28, 2019
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6AL0
 | | The NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicus S2P homolog with the PA12 tag inserted between the residues 263 and 267 | | Descriptor: | Heavy chain of antigen binding fragment, Fab of NZ-1, Light chain of antigen binding fragment, ... | | Authors: | Tamura, R, Oi, R, Kaneko, M.K, Kato, Y, Nogi, T. | | Deposit date: | 2018-09-05 | | Release date: | 2019-02-13 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Application of the NZ-1 Fab as a crystallization chaperone for PA tag-inserted target proteins.
Protein Sci., 28, 2019
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1JWG
 | | VHS Domain of human GGA1 complexed with cation-independent M6PR C-terminal Peptide | | Descriptor: | ADP-ribosylation factor binding protein GGA1, Cation-independent mannose-6-phosphate receptor, IODIDE ION | | Authors: | Shiba, T, Takatsu, H, Nogi, T, Matsugaki, N, Kawasaki, M, Igarashi, N, Suzuki, M, Kato, R, Earnest, T, Nakayama, K, Wakatsuki, S. | | Deposit date: | 2001-09-04 | | Release date: | 2002-03-06 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural basis for recognition of acidic-cluster dileucine sequence by GGA1.
Nature, 415, 2002
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1JWF
 | | Crystal Structure of human GGA1 VHS domain. | | Descriptor: | ADP-ribosylation factor binding protein GGA1 | | Authors: | Shiba, T, Takatsu, H, Nogi, T, Matsugaki, N, Kawasaki, M, Igarashi, N, Suzuki, M, Kato, R, Earnest, T, Nakayama, K, Wakatsuki, S. | | Deposit date: | 2001-09-04 | | Release date: | 2002-03-06 | | Last modified: | 2018-06-20 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Structural basis for recognition of acidic-cluster dileucine sequence by GGA1.
Nature, 415, 2002
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1J2J
 | | Crystal structure of GGA1 GAT N-terminal region in complex with ARF1 GTP form | | Descriptor: | ADP-ribosylation factor 1, ADP-ribosylation factor binding protein GGA1, GUANOSINE-5'-TRIPHOSPHATE, ... | | Authors: | Shiba, T, Kawasaki, M, Takatsu, H, Nogi, T, Matsugaki, N, Igarashi, N, Suzuki, M, Kato, R, Nakayama, K, Wakatsuki, S. | | Deposit date: | 2003-01-05 | | Release date: | 2003-05-06 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Molecular mechanism of membrane recruitment of GGA by ARF in lysosomal protein transport
NAT.STRUCT.BIOL., 10, 2003
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1O3Y
 | | Crystal structure of mouse ARF1 (delta17-Q71L), GTP form | | Descriptor: | ADP-ribosylation factor 1, GUANOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION | | Authors: | Shiba, T, Kawasaki, M, Takatsu, H, Nogi, T, Matsugaki, N, Igarashi, N, Suzuki, M, Kato, R, Nakayama, K, Wakatsuki, S. | | Deposit date: | 2003-05-08 | | Release date: | 2003-05-20 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Molecular mechanism of membrane recruitment of GGA by ARF in lysosomal protein transport
Nat.Struct.Biol., 10, 2003
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3AFC
 | | Mouse Semaphorin 6A extracellular domain | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Semaphorin-6A | | Authors: | Yasui, N, Nogi, T, Mihara, E, Takagi, J. | | Deposit date: | 2010-02-26 | | Release date: | 2010-10-06 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Structural basis for semaphorin signalling through the plexin receptor.
Nature, 467, 2010
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3VI3
 | | Crystal structure of alpha5beta1 integrin headpiece (ligand-free form) | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, ... | | Authors: | Nagae, M, Nogi, T, Takagi, J. | | Deposit date: | 2011-09-21 | | Release date: | 2012-02-22 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Crystal structure of alpha5beta1 integrin ectodomain: Atomic details of the fibronectin receptor
J.Cell Biol., 197, 2012
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3VI4
 | | Crystal structure of alpha5beta1 integrin headpiece in complex with RGD peptide | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, ... | | Authors: | Nagae, M, Nogi, T, Takagi, J. | | Deposit date: | 2011-09-21 | | Release date: | 2012-02-22 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Crystal structure of alpha5beta1 integrin ectodomain: Atomic details of the fibronectin receptor
J.Cell Biol., 197, 2012
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2ZOU
 | | Crystal structure of human F-spondin reeler domain (fragment 2) | | Descriptor: | 1,2-ETHANEDIOL, Spondin-1 | | Authors: | Nagae, M, Nogi, T, Takagi, J. | | Deposit date: | 2008-06-07 | | Release date: | 2008-10-14 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Structure of the F-spondin reeler domain reveals a unique beta-sandwich fold with a deformable disulfide-bonded loop
Acta Crystallogr.,Sect.D, 64, 2008
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2ZOT
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3A7Q
 | | Structural basis for specific recognition of reelin by its receptors | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, ... | | Authors: | Yasui, N, Nogi, T, Takagi, J. | | Deposit date: | 2009-10-01 | | Release date: | 2010-03-23 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Structural Basis for Specific Recognition of Reelin by Its Receptors
Structure, 18, 2010
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3ASI
 | | Alpha-Neurexin-1 ectodomain fragment; LNS5-EGF3-LNS6 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, Neurexin-1-alpha | | Authors: | Tanaka, H, Nogi, T, Yasui, N, Takagi, J. | | Deposit date: | 2010-12-13 | | Release date: | 2011-04-13 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structural Basis for Variant-Specific Neuroligin-Binding by alpha-Neurexin
Plos One, 6, 2011
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3VKF
 | | Crystal Structure of Neurexin 1beta/Neuroligin 1 complex | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, Neurexin-1-beta, ... | | Authors: | Tanaka, H, Miyazaki, N, Nogi, T, Iwasaki, K, Takagi, J. | | Deposit date: | 2011-11-15 | | Release date: | 2012-08-01 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (3.3 Å) | | Cite: | Higher-order architecture of cell adhesion mediated by polymorphic synaptic adhesion molecules neurexin and neuroligin.
Cell Rep, 2, 2012
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3WSY
 | | SorLA Vps10p domain in complex with its own propeptide fragment | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Sortilin-related receptor, peptide from Sortilin-related receptor | | Authors: | Kitago, Y, Nakata, Z, Nagae, M, Nogi, T, Takagi, J. | | Deposit date: | 2014-03-30 | | Release date: | 2015-02-04 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.11 Å) | | Cite: | Structural basis for amyloidogenic peptide recognition by sorLA.
Nat.Struct.Mol.Biol., 22, 2015
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3WSX
 | | SorLA Vps10p domain in ligand-free form | | Descriptor: | 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, PHOSPHATE ION, ... | | Authors: | Kitago, Y, Nakata, Z, Nagae, M, Nogi, T, Takagi, J. | | Deposit date: | 2014-03-30 | | Release date: | 2015-02-04 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.35 Å) | | Cite: | Structural basis for amyloidogenic peptide recognition by sorLA.
Nat.Struct.Mol.Biol., 22, 2015
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3WSZ
 | | SorLA Vps10p domain in complex with Abeta-derived peptide | | Descriptor: | 10-mer peptide, 2-acetamido-2-deoxy-beta-D-glucopyranose, Sortilin-related receptor | | Authors: | Kitago, Y, Nakata, Z, Nagae, M, Nogi, T, Takagi, J. | | Deposit date: | 2014-03-30 | | Release date: | 2015-02-04 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (3.201 Å) | | Cite: | Structural basis for amyloidogenic peptide recognition by sorLA.
Nat.Struct.Mol.Biol., 22, 2015
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