PDB Search results for query - Protein Data Bank Japan

PDB: 113 results

Structure of human 2E01 Fab in complex with influenza virus neuraminidase from B/Phuket/3073/2013
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Antibody Fab heavy chain, Antibody Fab light chain, ...
Authors:	Dai, Y.N, Fremont, D.H, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2019-11-28
Release date:	2020-10-07
Last modified:	2020-10-28
Method:	ELECTRON MICROSCOPY (2.8 Å)
Cite:	Human Antibodies Targeting Influenza B Virus Neuraminidase Active Site Are Broadly Protective. Immunity, 53, 2020

6W37

STRUCTURE OF THE SARS-CoV-2 ORF7A ENCODED ACCESSORY PROTEIN
Descriptor:	ORF7a protein
Authors:	Nelson, C.A, Minasov, G, Shuvalova, L, Fremont, D.H, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2020-03-09
Release date:	2020-04-29
Last modified:	2023-10-18
Method:	X-RAY DIFFRACTION (2.9 Å)
Cite:	STRUCTURE OF THE SARS-CoV-2 ORF7A ENCODED ACCESSORY PROTEIN To be published

6PLK

Crystal structure of ZIKV-116 Fab in complex with ZIKV envelope DIII
Descriptor:	Env, ZIKV-116 heavy chain, ZIKV-116 light chain
Authors:	Zhao, H, Fremont, D.H, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2019-07-01
Release date:	2019-11-20
Last modified:	2023-10-11
Method:	X-RAY DIFFRACTION (2.3 Å)
Cite:	Mechanism of differential Zika and dengue virus neutralization by a public antibody lineage targeting the DIII lateral ridge. J.Exp.Med., 217, 2020

6P6P

Crystal structure of hemagglutinin from influenza virus A/Sichuan/2/1987 (H3N2)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Hemagglutinin, beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Authors:	Dai, Y.N, Fremont, D.H, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2019-06-04
Release date:	2020-07-01
Last modified:	2023-10-11
Method:	X-RAY DIFFRACTION (2.31 Å)
Cite:	Crystal structure of hemagglutinin from influenza virus A/Sichuan/2/1987 (H3N2) To Be Published

5KVG

Zika specific antibody, ZV-67, bound to ZIKA envelope DIII
Descriptor:	CHLORIDE ION, ZIKA Envelope DIII, ZV-67 Antibody Fab Heavy Chain, ...
Authors:	Zhao, H, Nelson, C.A, Fremont, D.H, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2016-07-14
Release date:	2016-08-03
Last modified:	2016-08-24
Method:	X-RAY DIFFRACTION (1.4 Å)
Cite:	Structural Basis of Zika Virus-Specific Antibody Protection. Cell, 166, 2016

5KVF

Zika specific antibody, ZV-64, bound to ZIKA envelope DIII
Descriptor:	GLYCEROL, ZV-64 Antibody Fab Heavy Chain, ZV-64 Antibody Fab Light Chain, ...
Authors:	Zhao, H, Nelson, C.A, Fremont, D.H, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2016-07-14
Release date:	2016-08-03
Last modified:	2016-08-24
Method:	X-RAY DIFFRACTION (1.4 Å)
Cite:	Structural Basis of Zika Virus-Specific Antibody Protection. Cell, 166, 2016

5KVE

Zika specific antibody, ZV-48, bound to ZIKA envelope DIII
Descriptor:	1,2-ETHANEDIOL, ACETATE ION, Genome polyprotein, ...
Authors:	Zhao, H, Nelson, C.A, Fremont, D.H, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2016-07-14
Release date:	2016-08-10
Last modified:	2019-12-25
Method:	X-RAY DIFFRACTION (1.7 Å)
Cite:	Structural Basis of Zika Virus-Specific Antibody Protection. Cell, 166, 2016

5KVD

Zika specific antibody, ZV-2, bound to ZIKA envelope DIII
Descriptor:	1,2-ETHANEDIOL, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, SODIUM ION, ...
Authors:	Zhao, H, Nelson, C.A, Fremont, D.H, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2016-07-14
Release date:	2016-08-03
Last modified:	2016-08-24
Method:	X-RAY DIFFRACTION (1.65 Å)
Cite:	Structural Basis of Zika Virus-Specific Antibody Protection. Cell, 166, 2016

2NYZ

Viral Chemokine Binding Protein M3 From Murine Gammaherpesvirus68 In Complex With The C- Chemokine XCL1
Descriptor:	Hypothetical protein GAMMAHV.M3, Lymphotactin
Authors:	Alexander-Brett, J.M, Fremont, D.H.
Deposit date:	2006-11-21
Release date:	2007-12-25
Last modified:	2023-08-30
Method:	X-RAY DIFFRACTION (2.6 Å)
Cite:	Dual GPCR and GAG mimicry by the M3 chemokine decoy receptor. J.Exp.Med., 204, 2007

7MKM

SARS-CoV-2 Spike RBD in complex with neutralizing Fab SARS2-38 (local refinement)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, SARS2-38 Fv heavy chain, SARS2-38 Fv light chain, ...
Authors:	Adams, L.J, Fremont, D.H, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2021-04-24
Release date:	2021-05-12
Last modified:	2021-12-01
Method:	ELECTRON MICROSCOPY (3.16 Å)
Cite:	A potently neutralizing SARS-CoV-2 antibody inhibits variants of concern by utilizing unique binding residues in a highly conserved epitope. Immunity, 54, 2021

7MKL

SARS-CoV-2 Spike in complex with neutralizing Fab SARS2-38 (three down conformation)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, SARS2-38 Fv heavy chain, ...
Authors:	Adams, L.J, Fremont, D.H, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2021-04-24
Release date:	2021-05-12
Last modified:	2021-12-01
Method:	ELECTRON MICROSCOPY (3.2 Å)
Cite:	A potently neutralizing SARS-CoV-2 antibody inhibits variants of concern by utilizing unique binding residues in a highly conserved epitope. Immunity, 54, 2021

2NZ1

Viral Chemokine Binding Protein M3 From Murine Gammaherpesvirus68 In Complex With The CC-Chemokine CCL2/MCP-1
Descriptor:	Hypothetical protein GAMMAHV.M3, Small inducible cytokine A2
Authors:	Alexander-Brett, J.M, Fremont, D.H.
Deposit date:	2006-11-22
Release date:	2007-12-25
Last modified:	2023-08-30
Method:	X-RAY DIFFRACTION (2.5 Å)
Cite:	Dual GPCR and GAG mimicry by the M3 chemokine decoy receptor. J.Exp.Med., 204, 2007

2R29

Neutralization of dengue virus by a serotype cross-reactive antibody elucidated by cryoelectron microscopy and x-ray crystallography
Descriptor:	Envelope protein E, Heavy chain of Fab 1A1D-2, Light chain of Fab 1A1D-2
Authors:	Lok, S.M, Kostyuchenko, V.K, Nybakken, G.E, Holdaway, H.A, Battisti, A.J, Sukupolvi-petty, S, Sedlak, D, Fremont, D.H, Chipman, P.R, Roehrig, J.T, Diamond, M.S, Kuhn, R.J, Rossmann, M.G.
Deposit date:	2007-08-24
Release date:	2007-12-25
Last modified:	2018-01-24
Method:	X-RAY DIFFRACTION (3 Å)
Cite:	Binding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins. Nat.Struct.Mol.Biol., 15, 2008

2HG0

Structure of the West Nile Virus envelope glycoprotein
Descriptor:	2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, Envelope glycoprotein
Authors:	Nybakken, G.E, Nelson, C.A, Chen, B.R, Diamond, M.S, Fremont, D.H.
Deposit date:	2006-06-26
Release date:	2006-11-07
Last modified:	2023-08-30
Method:	X-RAY DIFFRACTION (3 Å)
Cite:	Crystal structure of the West Nile virus envelope glycoprotein. J.Virol., 80, 2006

2GRK

Crystal structure of ectromelia virus EVM1 chemokine binding protein
Descriptor:	EVM001
Authors:	Arnold, P.L, Fremont, D.H.
Deposit date:	2006-04-24
Release date:	2006-05-09
Last modified:	2023-08-30
Method:	X-RAY DIFFRACTION (2.6 Å)
Cite:	Structural determinants of chemokine binding by an ectromelia virus-encoded decoy receptor. J.Virol., 80, 2006

4OIE

West Nile Virus Non-structural Protein NS1
Descriptor:	GLYCEROL, NON-STRUCTURAL PROTEIN NS1
Authors:	Edeling, M.A, Fremont, D.H, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2014-01-19
Release date:	2014-03-05
Last modified:	2014-04-23
Method:	X-RAY DIFFRACTION (1.85 Å)
Cite:	Structural basis of Flavivirus NS1 assembly and antibody recognition. Proc.Natl.Acad.Sci.USA, 111, 2014

4OII

West Nile Virus NS1 in complex with neutralizing 22NS1 antibody Fab
Descriptor:	Heavy Chain of Fab fragment of 22NS1 Antibody, Light Chain of Fab fragment of 22NS1 Antibody, NON-STRUCTURAL PROTEIN NS1
Authors:	Edeling, M.A, Fremont, D.H, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2014-01-19
Release date:	2014-03-05
Last modified:	2017-11-22
Method:	X-RAY DIFFRACTION (3 Å)
Cite:	Structural basis of Flavivirus NS1 assembly and antibody recognition. Proc.Natl.Acad.Sci.USA, 111, 2014

4PDC

Crystal structure of Cowpox virus CPXV018 (OMCP) bound to human NKG2D
Descriptor:	CPXV018 protein, NKG2-D type II integral membrane protein
Authors:	Lazear, E, Nelson, C.A, Fremont, D.H, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2014-04-17
Release date:	2014-05-21
Last modified:	2023-09-27
Method:	X-RAY DIFFRACTION (1.991 Å)
Cite:	Structural basis of cowpox evasion of NKG2D immunosurveillance Biorxiv, 2019

4OIG

Dengue Virus Non-structural Protein NS1
Descriptor:	Non-structural protein 1, NS1, SULFATE ION
Authors:	Edeling, M.A, Fremont, D.H, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2014-01-19
Release date:	2014-03-05
Last modified:	2017-11-22
Method:	X-RAY DIFFRACTION (2.69 Å)
Cite:	Structural basis of Flavivirus NS1 assembly and antibody recognition. Proc.Natl.Acad.Sci.USA, 111, 2014

3P54

Crystal Structure of the Japanese Encephalitis Virus Envelope Protein, strain SA-14-14-2.
Descriptor:	envelope glycoprotein
Authors:	Luca, V.C, Nelson, C.A, AbiMansour, J.P, Diamond, M.S, Fremont, D.H, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2010-10-07
Release date:	2010-12-08
Last modified:	2012-02-08
Method:	X-RAY DIFFRACTION (2.097 Å)
Cite:	Crystal structure of the Japanese encephalitis virus envelope protein. J.Virol., 86, 2012

6C74

Crystal Structure of Murine CD300lf in complex with phosphocholine
Descriptor:	CALCIUM ION, CMRF35-like molecule-1, PHOSPHOCHOLINE
Authors:	Nelson, C.A, Fremont, D.H.
Deposit date:	2018-01-19
Release date:	2018-09-12
Last modified:	2023-10-04
Method:	X-RAY DIFFRACTION (1.358 Å)
Cite:	Structural basis for murine norovirus engagement of bile acids and the CD300lf receptor. Proc. Natl. Acad. Sci. U.S.A., 115, 2018

6C6Q

Crystal Structure of the Murine Norovirus VP1 P Domain in complex with the CD300lf Receptor
Descriptor:	1,2-ETHANEDIOL, CHLORIDE ION, CMRF35-like molecule 1, ...
Authors:	Nelson, C.A, Fremont, D.H.
Deposit date:	2018-01-19
Release date:	2018-09-12
Last modified:	2023-10-04
Method:	X-RAY DIFFRACTION (2 Å)
Cite:	Structural basis for murine norovirus engagement of bile acids and the CD300lf receptor. Proc. Natl. Acad. Sci. U.S.A., 115, 2018

1FNG

HISTOCOMPATIBILITY ANTIGEN
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, PROTEIN (MHC CLASS II I-EK, ALPHA CHAIN), ...
Authors:	Miley, M.J, Nelson, C.A, Fremont, D.H.
Deposit date:	2000-08-21
Release date:	2001-03-07
Last modified:	2020-07-29
Method:	X-RAY DIFFRACTION (1.9 Å)
Cite:	Structural and functional consequences of altering a peptide MHC anchor residue. J.Immunol., 166, 2001

7K9J

SARS-CoV-2 Spike in complex with neutralizing Fab 2H04 (three down conformation)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2H04 heavy chain, ...
Authors:	Errico, J.M, Fremont, D.H, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2020-09-29
Release date:	2021-09-29
Last modified:	2021-11-10
Method:	ELECTRON MICROSCOPY (3 Å)
Cite:	Structural mechanism of SARS-CoV-2 neutralization by two murine antibodies targeting the RBD. Cell Rep, 37, 2021

7K9K

SARS-CoV-2 Spike RBD in complex with neutralizing Fab 2H04 (local refinement)
Descriptor:	2H04 heavy chain, 2H04 light chain, Spike protein S1, ...
Authors:	Errico, J.M, Fremont, D.H, Center for Structural Genomics of Infectious Diseases (CSGID)
Deposit date:	2020-09-29
Release date:	2021-09-29
Last modified:	2021-11-10
Method:	ELECTRON MICROSCOPY (3.14 Å)
Cite:	Structural mechanism of SARS-CoV-2 neutralization by two murine antibodies targeting the RBD. Cell Rep, 37, 2021

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Total results:	113
Displayed results:	25
Sorted by:	Hit score (from highest)
Deposition authors:	"Fremont, D.H."