New PDB entries

The structure of the junction region of the wild-type murine native cardiac thin filament in Ca2+-free state
Descriptor:	ADENOSINE-5'-DIPHOSPHATE, Actin, alpha cardiac muscle 1, ...
Authors:	Galkin, V.E, Risi, C.M.
Deposit date:	2024-10-22
Release date:	2025-06-04
Method:	ELECTRON MICROSCOPY (4 Å)
Cite:	The structure of the junction region of the murine wild-type native cardiac thin filament. To Be Published

9EG7

X-ray diffraction structure of papain co-crystallized with E64-C
Descriptor:	N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-2-METHYL-BUTANE, Papain
Authors:	Vlahakis, N.W, Rodriguez, J.A, Tang, Y.
Deposit date:	2024-11-20
Release date:	2025-06-04
Method:	X-RAY DIFFRACTION (1.5 Å)
Cite:	Enzymatic combinatorial synthesis of E-64 and related cysteine protease inhibitors. Nat.Chem.Biol., 2025

9ELJ

Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11+Q493E+S31deletion spike protein (one RBD up state)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
Authors:	Feng, Z, Huang, J, Ward, A.B.
Deposit date:	2024-12-04
Release date:	2025-06-04
Method:	ELECTRON MICROSCOPY (2.92 Å)
Cite:	Structure of SARS-CoV-2 KP.3.1.1 Spike Protein To Be Published

9ELK

Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11+Q493E+S31deletion spike protein (closed state)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
Authors:	Feng, Z, Huang, J, Ward, A.B.
Deposit date:	2024-12-04
Release date:	2025-06-04
Method:	ELECTRON MICROSCOPY (2.82 Å)
Cite:	Structure of SARS-CoV-2 KP.3.1.1 Spike Protein To Be Published

9ELL

Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11 spike protein (one RBD up state)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
Authors:	Feng, Z, Huang, J, Ward, A.B.
Deposit date:	2024-12-04
Release date:	2025-06-04
Method:	ELECTRON MICROSCOPY (2.93 Å)
Cite:	Structure of SARS-CoV-2 KP.3.1.1 Spike Protein To Be Published

9ELM

Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11 spike protein (closed state)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
Authors:	Feng, Z, Huang, J, Ward, A.B.
Deposit date:	2024-12-04
Release date:	2025-06-04
Method:	ELECTRON MICROSCOPY (2.68 Å)
Cite:	Structure of SARS-CoV-2 KP.3.1.1 Spike Protein To Be Published

9ENA

Lysosomal glucocerebrosidase in complex with a stabilizing nanobody
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Chains: B, ...
Authors:	Dal Maso, T, Versees, W.
Deposit date:	2024-03-12
Release date:	2025-06-04
Method:	X-RAY DIFFRACTION (1.7 Å)
Cite:	Developing nanobodies as allosteric molecular chaperones of glucocerebrosidase function. Nat Commun, 16, 2025

9F0X

CryoEM structure of the F plasmid relaxosome in its pre-initiation state, derived from the ds-27_+143-R Locally-refined Map 3.76 A
Descriptor:	Integration host factor subunit alpha, Integration host factor subunit beta, Multifunctional conjugation protein TraI, ...
Authors:	Williams, S.M, Waksman, G.
Deposit date:	2024-04-17
Release date:	2025-06-04
Method:	ELECTRON MICROSCOPY (3.78 Å)
Cite:	Cryo-EM Structure of the relaxosome, a complex essential for bacterial mating and the spread of antibiotic resistance genes. Nat Commun, 16, 2025

9F0Y

CryoEM map of the F plasmid relaxosome with TraI in its TE mode. ss-27_+8ds+9_+143-R Locally-refined 3.45 A Map
Descriptor:	Integration host factor subunit alpha, Integration host factor subunit beta, MAGNESIUM ION, ...
Authors:	Williams, S.M, Waksman, G.
Deposit date:	2024-04-17
Release date:	2025-06-04
Method:	ELECTRON MICROSCOPY (3.45 Å)
Cite:	Cryo-EM Structure of the relaxosome, a complex essential for bacterial mating and the spread of antibiotic resistance genes. Nat Commun, 16, 2025

9F0Z

CryoEM structure of the F plasmid relaxosome with truncated TraI1-863 in its TE mode, derived from the ss-27_+8ds+9_+143-R_deltaAH+CTD Locally-refined 3.42 A Map
Descriptor:	Integration host factor subunit alpha, Integration host factor subunit beta, MAGNESIUM ION, ...
Authors:	Williams, S.M, Waksman, G.
Deposit date:	2024-04-17
Release date:	2025-06-04
Method:	ELECTRON MICROSCOPY (3.42 Å)
Cite:	Cryo-EM Structure of the relaxosome, a complex essential for bacterial mating and the spread of antibiotic resistance genes. Nat Commun, 16, 2025

9F10

CryoEM structure of the F plasmid relaxosome with TraI in its TE mode, without accessory protein TraM. Derived from the ss-27_+8ds+9_+143-R_deltaTraM Locally-refined 2.94 A Map.
Descriptor:	Integration host factor subunit alpha, Integration host factor subunit beta, MAGNESIUM ION, ...
Authors:	Williams, S.M, Waksman, G.
Deposit date:	2024-04-17
Release date:	2025-06-04
Method:	ELECTRON MICROSCOPY (2.94 Å)
Cite:	Cryo-EM Structure of the relaxosome, a complex essential for bacterial mating and the spread of antibiotic resistance genes. Nat Commun, 16, 2025

9F11

CryoEM structure of the F plasmid relaxosome with oriT DNA ss-27_+3ds+4_+143 and TraI its TE mode, derived from ss-27_+3ds+4_+143-R Locally-refined 3.68 A Map.
Descriptor:	Integration host factor subunit alpha, Integration host factor subunit beta, MAGNESIUM ION, ...
Authors:	Williams, S.M, Waksman, G.
Deposit date:	2024-04-17
Release date:	2025-06-04
Method:	ELECTRON MICROSCOPY (3.68 Å)
Cite:	Cryo-EM Structure of the relaxosome, a complex essential for bacterial mating and the spread of antibiotic resistance genes. Nat Commun, 16, 2025

9F12

CryoEM structure of the F plasmid relaxosome with oriT DNA ss-27_-3ds-2_+143 and TraI its TE mode, derived from ss-27_-3ds-2_+143-R Locally-refined 3.42 A Map.
Descriptor:	Integration host factor subunit alpha, Integration host factor subunit beta, MAGNESIUM ION, ...
Authors:	Williams, S.M, Waksman, G.
Deposit date:	2024-04-17
Release date:	2025-06-04
Method:	ELECTRON MICROSCOPY (3.42 Å)
Cite:	Cryo-EM Structure of the relaxosome, a complex essential for bacterial mating and the spread of antibiotic resistance genes. Nat Commun, 16, 2025

9FDM

Structure of the toxin Schistosomine 79 from Schistosoma
Descriptor:	BIOTIN, SODIUM ION, SULFATE ION, ...
Authors:	Morera, S, Vigouroux, A.
Deposit date:	2024-05-17
Release date:	2025-06-04
Method:	X-RAY DIFFRACTION (2.099 Å)
Cite:	To be determined later To Be Published

9FEM

mNeonGreen - Directionality of Optical Properties of Fluorescent Proteins
Descriptor:	SULFATE ION, mNeonGreen
Authors:	Myskova, J, Brynda, J, Lazar, J.
Deposit date:	2024-05-21
Release date:	2025-06-04
Method:	X-RAY DIFFRACTION (2.32 Å)
Cite:	Directionality of Optical Properties of Fluorescent Proteins To Be Published

9FEN

LSSmOrange (P1) - Directionality of Optical Properties of Fluorescent Proteins
Descriptor:	nowGFP crystallized in Space Group C2
Authors:	Myskova, J, Brynda, J, Lazar, J.
Deposit date:	2024-05-21
Release date:	2025-06-04
Method:	X-RAY DIFFRACTION (1.6 Å)
Cite:	Directionality of Optical Properties of Fluorescent Proteins To Be Published

9FEO

LSSmOrange (P1) - Directionality of Optical Properties of Fluorescent Proteins
Descriptor:	mOrange
Authors:	Myskova, J, Brynda, J, Lazar, J.
Deposit date:	2024-05-21
Release date:	2025-06-04
Method:	X-RAY DIFFRACTION (1.9 Å)
Cite:	Directionality of Optical Properties of Fluorescent Proteins To Be Published

9FEQ

LSSmOrange (P1) - Directionality of Optical Properties of Fluorescent Proteins
Descriptor:	CALCIUM ION, DI(HYDROXYETHYL)ETHER, PHOSPHATE ION, ...
Authors:	Myskova, J, Brynda, J, Lazar, J.
Deposit date:	2024-05-21
Release date:	2025-06-04
Method:	X-RAY DIFFRACTION (1.6 Å)
Cite:	Directionality of Optical Properties of Fluorescent Proteins To Be Published

9FER

wasCFP (SG P21) - Directionality of Optical Properties of Fluorescent Proteins
Descriptor:	Fluorescent protein plum
Authors:	Myskova, J, Brynda, J, Lazar, J.
Deposit date:	2024-05-21
Release date:	2025-06-04
Method:	X-RAY DIFFRACTION (1.65 Å)
Cite:	Directionality of Optical Properties of Fluorescent Proteins To Be Published

9FES

mCherry - Directionality of Optical Properties of Fluorescent Proteins
Descriptor:	MCHERRY
Authors:	Myskova, J, Brynda, J, Lazar, J.
Deposit date:	2024-05-21
Release date:	2025-06-04
Method:	X-RAY DIFFRACTION (1.66 Å)
Cite:	Directionality of Optical Properties of Fluorescent Proteins To Be Published

9FEU

Cryo-EM structure of the beta3 homomeric GABA(A) receptor in complex with HSM in the long-lived symmetric desensitised state
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, ...
Authors:	Mihaylov, D.B, Malinauskas, T, Aricescu, A.R.
Deposit date:	2024-05-21
Release date:	2025-06-04
Method:	ELECTRON MICROSCOPY (2.5 Å)
Cite:	Cryo-EM structure of the beta3 homomeric GABA(A) receptor in complex with HSM in the long-lived symmetric desensitised state To Be Published

9FEV

Cryo-EM structure of the beta3 homomeric GABA(A) receptor in the long-lived resting state
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Gamma-aminobutyric acid receptor subunit beta-3, ...
Authors:	Mihaylov, D.B, Malinauskas, T, Aricescu, A.R.
Deposit date:	2024-05-21
Release date:	2025-06-04
Method:	ELECTRON MICROSCOPY (3.1 Å)
Cite:	Cryo-EM structure of the beta3 homomeric GABA(A) receptor in the long-lived resting state To Be Published

9FEW

Cryo-EM structure of the beta3 homomeric GABA(A) receptor in the long-lived resting state (C1)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Gamma-aminobutyric acid receptor subunit beta-3, ...
Authors:	Mihaylov, D.B, Malinauskas, T, Aricescu, A.R.
Deposit date:	2024-05-21
Release date:	2025-06-04
Method:	ELECTRON MICROSCOPY (3.5 Å)
Cite:	Cryo-EM structure of the beta3 homomeric GABA(A) receptor in the long-lived resting state (C1) To Be Published

9FEX

Cryo-EM structure of the beta3 homomeric GABA(A) receptor in complex with HSM in the short-lived symmetric pre-active state (C5)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, ...
Authors:	Mihaylov, D.B, Malinauskas, T, Aricescu, A.R.
Deposit date:	2024-05-21
Release date:	2025-06-04
Method:	ELECTRON MICROSCOPY (2.6 Å)
Cite:	Cryo-EM structure of the beta3 homomeric GABA(A) receptor in complex with HSM in the short-lived symmetric pre-active state (C5) To Be Published

9FEY

Cryo-EM structure of the beta3 homomeric GABA(A) receptor in complex with HSM in the short-lived symmetric pre-active state (C1)
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, ...
Authors:	Mihaylov, D.B, Malinauskas, T, Aricescu, A.R.
Deposit date:	2024-05-21
Release date:	2025-06-04
Method:	ELECTRON MICROSCOPY (2.9 Å)
Cite:	Cryo-EM structure of the beta3 homomeric GABA(A) receptor in complex with HSM in the short-lived symmetric pre-active state (C1) To Be Published

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