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The Electron Microscopy Data Bank (EMDB) at PDBe

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Introduction

The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography.

The EMDB was founded at EBI in 2002, under the leadership of Kim Henrick. Since 2007 it has been operated jointly by the PDBe, and the Research Collaboratory for Structural Bioinformatics (RCSB PDB) as a part of EMDataBank which is funded by a joint NIH grant to PDBe, the RCSB and the National Center for Macromolecular Imaging (NCMI).


EMDataResource

A wealth of additional resources can be found at EMDataResource including:


Gallery of recent structures

15113 released maps, and 4719 associated publications. Last update: 2021-05-05 - 147 maps released this week


  1. EMD-11082
    EMD-11082
    Cryo-EM structure of the A. baumannii MlaBDEF complex bound to APPNHP
  2. EMD-11083
    EMD-11083
    Cryo-EM structure of the Acinetobacter baumannii MlaBDEF complex
  3. EMD-11396
    EMD-11396
    Human mitochondrial ribosome in complex with mRNA and P/E-tRNA
  4. EMD-11715
    EMD-11715
    Cryo-EM reconstruction of the di-hexameric endocytic adaptor complex AENTH (ENTH F5A/L12A/V13A mutant)
  5. EMD-11987
    EMD-11987
    Structure of the endocytic adaptor complex AENTH
  6. EMD-12183
    EMD-12183
    Salmonella LP ring 26 mer refined in C26 map
  7. EMD-12190
    EMD-12190
    In situ assembled Salmonella FlgD hook cap complex
  8. EMD-12192
    EMD-12192
    Salmonella export gate and rod refined in focussed C1 map
  9. EMD-12193
    EMD-12193
    Salmonella flagellar basal body assembly intermediate - P ring alone structure
  10. EMD-12195
    EMD-12195
    Salmonella FliF ring (34mer) in intact basal body - C1
  11. EMD-12287
    EMD-12287
    HIV-1 Gag T8I NC-RNA layer
  12. EMD-12331
    EMD-12331
    LsaA, an antibiotic resistance ABCF, in complex with 70S ribosome from Enterococcus faecalis
  13. EMD-12332
    EMD-12332
    VgaA-LC, an antibiotic resistance ABCF, in complex with 70S ribosome from Staphylococcus aureus
  14. EMD-12333
    EMD-12333
    70S ribosome from Staphylococcus aureus
  15. EMD-12334
    EMD-12334
    VgaL, an antibiotic resistance ABCF, in complex with 70S ribosome from Listeria monocytogenes
  16. EMD-12335
    EMD-12335
    Structure of PSII-M
  17. EMD-12336
    EMD-12336
    Structure of PSII-I (PSII with Psb27, Psb28, and Psb34)
  18. EMD-12337
    EMD-12337
    Structure of PSII-I prime (PSII with Psb28, and Psb34)
  19. EMD-12374
    EMD-12374
    Tomogram of mutant huntingtin inclusion (recruitment foci) in the cytoplasm of hippocampal CA1 neuron in 6 month old zQ175 mice
  20. EMD-12376
    EMD-12376
    Mutant huntingtin containing organelle resembles MVB in 6-month-old zQ175 mice
  21. EMD-12527
    EMD-12527
    55S mammalian mitochondrial ribosome with mtRF1a and P-site tRNAMet
  22. EMD-12529
    EMD-12529
    55S mammalian mitochondrial ribosome with ICT1 and P site tRNAMet
  23. EMD-12534
    EMD-12534
    Structure of the yeast Gcn1 bound to a leading stalled 80S ribosome with Rbg2, Gir2, A- and P-tRNA and eIF5A
  24. EMD-12536
    EMD-12536
    Tomogram of mutant huntingtin containing organelle resembles autolysosome in 6-month-old zQ175 mice
  25. EMD-12537
    EMD-12537
    Structure of human CTLH SR4 complex
  26. EMD-12538
    EMD-12538
    Structure of endogenous yeast GID Ant complex
  27. EMD-12539
    EMD-12539
    Tomogram of mutant huntingtin containing organelle resembles autolysosome/residual body in 6-month-old zQ175 mice
  28. EMD-12540
    EMD-12540
    Structure of endogenous yeast Chelator-GID Ant complex
  29. EMD-12541
    EMD-12541
    Structure of Apo Chelator-GID SR4 E3 ubiquitin ligase
  30. EMD-12542
    EMD-12542
    Structure of human CTLH-WDR26 supramolecular assembly
  31. EMD-12545
    EMD-12545
    Structure of supramolecular assembly and substrate receptor scaffolding modules of human CTLH-WDR26 complex
  32. EMD-12547
    EMD-12547
    Structure of supramolecular assembly and substrate receptor scaffolding modules of human CTLH-MKLN1 complex
  33. EMD-12548
    EMD-12548
    Structure of GID SR4 complex
  34. EMD-12557
    EMD-12557
    Structure of yeast Chelator-GID SR4 E3 ubiquitin ligase bound to its tetrameric metabolic enzyme substrate Fbp1
  35. EMD-12559
    EMD-12559
    Substrate receptor scaffolding module of yeast Chelator-GID SR4 E3 ubiquitin ligase bound to Fbp1 substrate
  36. EMD-12560
    EMD-12560
    Catalytic module of yeast Chelator-GID SR4 E3 ubiquitin ligase
  37. EMD-12563
    EMD-12563
    Supramolecular assembly module of yeast Chelator-GID SR4 E3 ubiquitin ligase
  38. EMD-12564
    EMD-12564
    Substrate receptor scaffolding module of human CTLH E3 ubiquitin ligase
  39. EMD-12567
    EMD-12567
    39S mammalian mitochondrial large ribosomal subunit with mtRRF (post) and mtEFG2
  40. EMD-12603
    EMD-12603
    Salmonella flagellar basal body refined in C1 map
  41. EMD-12609
    EMD-12609
    Human Mediator with RNA Polymerase II Stalk
  42. EMD-12610
    EMD-12610
    Human Mediator with RNA Polymerase II Pre-initiation complex
  43. EMD-12611
    EMD-12611
    RNA polymerase II core pre-initiation complex with closed promoter DNA in proximal position
  44. EMD-12612
    EMD-12612
    RNA polymerase II core pre-initiation complex with closed promoter DNA in distal position
  45. EMD-12613
    EMD-12613
    RNA polymerase II core pre-initiation complex with open promoter DNA
  46. EMD-12614
    EMD-12614
    XPB-containing part of TFIIH in a post-translocated state (with ADP-BeF3)
  47. EMD-12615
    EMD-12615
    TFIIH in a pre-translocated state (without ADP-BeF3)
  48. EMD-12616
    EMD-12616
    TFIIH in a post-translocated state (with ADP-BeF3)
  49. EMD-12617
    EMD-12617
    RNA polymerase II pre-initiation complex with closed promoter DNA in proximal position
  50. EMD-12618
    EMD-12618
    RNA polymerase II pre-initiation complex with closed promoter DNA in distal position
  51. EMD-12619
    EMD-12619
    RNA polymerase II pre-initiation complex with open promoter DNA
  52. EMD-12620
    EMD-12620
    Focused refinement of the core RNA polymerase II pre-initiation complex in a consensus CC state (without ADP-BeF3)
  53. EMD-12621
    EMD-12621
    Focused refinement of the core RNA polymerase II pre-initiation complex in a consensus OC state (with ADP-BeF3)
  54. EMD-12622
    EMD-12622
    Focused refinement of the upstream complex for the RNA polymerase II pre-initiation complex in a consensus CC state (without ADP-BeF3)
  55. EMD-12623
    EMD-12623
    Focused refinement of the upstream complex for the RNA polymerase II pre-initiation complex in a consensus OC state (with ADP-BeF3)
  56. EMD-12624
    EMD-12624
    Focused refinement of XPB containing part of TFIIH in pre-translocated state (without ADP-BeF3)
  57. EMD-12625
    EMD-12625
    Focused refinement of XPD containing part of TFIIH in pre-translocated state (without ADP-BeF3)
  58. EMD-12626
    EMD-12626
    Focused refinement of XPD containing part of TFIIH in post-translocated state (with ADP-BeF3)
  59. EMD-12627
    EMD-12627
    Focused refinement of the RNA polymerase II core pre-initiation complex in a consensus IC-like state (with ADP-BeF3)
  60. EMD-12628
    EMD-12628
    Focused refinement of the upstream complex for the RNA polymerase II pre-initiation complex in a consensus IC-like state (with ADP-BeF3)
  61. EMD-12629
    EMD-12629
    Focused refinement of the core RNA polymerase II pre-initiation complex with intermediary promoter DNA (with ADP-BeF3)
  62. EMD-12630
    EMD-12630
    RNA polymerase II pre-initiation complex with intermediary promoter DNA
  63. EMD-21161
    EMD-21161
    Pore-forming protein
  64. EMD-21932
    EMD-21932
    Apo KIF14[391-772] in complex with a microtubule
  65. EMD-21933
    EMD-21933
    KIF14[391-772] - ADP in complex with a microtubule
  66. EMD-21934
    EMD-21934
    KIF14[391-772] dimer two-heads-bound state - ADP-AlFx in complex with a microtubule
  67. EMD-21935
    EMD-21935
    KIF14[391-772] dimer two-heads-bound state - AMP-PNP in complex with a microtubule
  68. EMD-21936
    EMD-21936
    Apo KIF14[391-755] in complex with a microtubule
  69. EMD-21937
    EMD-21937
    KIF14[391-755] - ADP in complex with a microtubule
  70. EMD-21938
    EMD-21938
    KIF14[391-755] dimer two-heads-bound state - ADP-AlFx in complex with a microtubule
  71. EMD-21939
    EMD-21939
    KIF14[391-755] dimer two-heads-bound state - AMP-PNP in complex with a microtubule
  72. EMD-21940
    EMD-21940
    KIF14[391-748] - ADP in complex with a microtubule
  73. EMD-21941
    EMD-21941
    KIF14[391-748] - ADP-AlFx in complex with a microtubule
  74. EMD-21942
    EMD-21942
    KIF14[391-748] - AMP-PNP in complex with a microtubule
  75. EMD-21943
    EMD-21943
    Apo KIF14[391-743] in complex with a microtubule
  76. EMD-21944
    EMD-21944
    KIF14[391-743] - ADP in complex with a microtubule
  77. EMD-21945
    EMD-21945
    Kif14[391-743] - ADP-AlFx open state class in complex with a microtubule
  78. EMD-21946
    EMD-21946
    Kif14[391-743] - AMP-PNP open state class in complex with a microtubule
  79. EMD-21947
    EMD-21947
    Apo KIF14[391-735] in complex with a microtubule
  80. EMD-21948
    EMD-21948
    KIF14[391-735] - ADP-AlFx in complex with a microtubule
  81. EMD-21949
    EMD-21949
    KIF14[391-735] - ANP-PNP in complex with a microtubule
  82. EMD-22874
    EMD-22874
    Cryo-electron tomography and subtomographic averaging reveals ciliary defects underlying human RSPH1 primary ciliary dyskinesia
  83. EMD-22875
    EMD-22875
    Cryo-electron tomography and subtomographic averaging reveals ciliary defects underlying human RSPH4A primary ciliary dyskinesia
  84. EMD-22884
    EMD-22884
    Structure of the NiV F glycoprotein in complex with the 12B2 neutralizing antibody
  85. EMD-22885
    EMD-22885
    Structure of the HeV F glycoprotein in complex with the 1F5 neutralizing antibody
  86. EMD-22982
    EMD-22982
    Nucleocapsid protein from the SARS-CoV-2 coronavirus
  87. EMD-23392
    EMD-23392
    Cryo-EM structure of the Mpa hexamer in the presence of ATP and the Pup-FabD substrate
  88. EMD-23469
    EMD-23469
    SARS-CoV spike complexed with Fab CV38-142 (3 Fabs bound)
  89. EMD-23470
    EMD-23470
    SARS-CoV spike complexed with Fab CV38-142 (2 Fabs bound)
  90. EMD-23471
    EMD-23471
    SARS-CoV-2 spike complexed with Fab CV38-142 (3 Fabs bound)
  91. EMD-23472
    EMD-23472
    SARS-CoV-2 spike complexed with Fab CV38-142 (2 Fabs bound)
  92. EMD-23511
    EMD-23511
    DNA-PKcs, Ku, DNA and LigIV N-BRCT in the NHEJ Long-range synaptic complex
  93. EMD-23512
    EMD-23512
    XLF, XRCC4 and LigIV C-BRCT in the NHEJ Long-range synaptic complex
  94. EMD-23513
    EMD-23513
    LigIV catalytic domain and distal Ku in the NHEJ Short-range synaptic complex
  95. EMD-23514
    EMD-23514
    Proximal Ku in NHEJ Short-range synaptic complex
  96. EMD-23515
    EMD-23515
    XLF, XRCC4 and LigIV BRCT in NHEJ Short-range synaptic complex
  97. EMD-23529
    EMD-23529
    Structure of the Marseillevirus nucleosome
  98. EMD-23530
    EMD-23530
    Marseillevirus heterotrimeric (hexameric) nucleosome
  99. EMD-23540
    EMD-23540
    KIF14[391-743] - AMP-PNP closed state class in complex with a microtubule
  100. EMD-23541
    EMD-23541
    KIF14[391-743] - ADP-AlFx closed state class in complex with a microtubule
  101. EMD-23566
    EMD-23566
    The SARS-CoV-2 spike protein receptor binding domain bound to neutralizing nanobodies WNb 2 and WNb 10
  102. EMD-23567
    EMD-23567
    Cryo-EM map of SARS-CoV-2 Spike protein bound to neutralising nanobodies WNb2 and WNb10 (C3 symmetry)
  103. EMD-23568
    EMD-23568
    Cryo-EM map of SARS-CoV-2 Spike protein in complex with neutralising nanobodies WNb2 and WNb10 (C1 symmetry)
  104. EMD-23613
    EMD-23613
    Cryo-EM structure of the Sema3A/PlexinA4/Neuropilin 1 complex
  105. EMD-23718
    EMD-23718
    Cryo-EM structure of Brazil (P.1) SARS-CoV-2 spike glycoprotein variant in the prefusion state (1 RBD up)
  106. EMD-30269
    EMD-30269
    Cryo-EM structure of the hE46K cross-seeded hWT alpha-synuclein fibril
  107. EMD-30352
    EMD-30352
    Split conformation 1 of CtHsp104 (Hsp104 from Chaetomium Thermophilum)
  108. EMD-30387
    EMD-30387
    Structure of Lassa virus polymerase bound to Z matrix protein
  109. EMD-30388
    EMD-30388
    Structure of Machupo virus polymerase bound to Z matrix protein (monomeric complex)
  110. EMD-30489
    EMD-30489
    Cryo-EM structure of the PGE2-bound EP2-Gs complex
  111. EMD-30490
    EMD-30490
    Cryo-EM structure of the Taprenepag-bound EP2-Gs complex
  112. EMD-30491
    EMD-30491
    Cryo-EM structure of the Evatanepag-bound EP2-Gs complex
  113. EMD-30599
    EMD-30599
    Cryo-EM structures of human GMPPA/GMPPB complex bound to GDP-Mannose
  114. EMD-30600
    EMD-30600
    Structure of a protein
  115. EMD-30628
    EMD-30628
    SARS-CoV-2 spike in complex with the CA521 neutralizing antibody (focused map)
  116. EMD-30629
    EMD-30629
    SARS-CoV-2 spike in complex with the CA521 neutralizing antibody (consensus map)
  117. EMD-30805
    EMD-30805
    Cryo-EM structure of Coxsackievirus B1 mature virion
  118. EMD-30806
    EMD-30806
    Cryo-EM structure of Coxsackievirus B1 empty particle
  119. EMD-30812
    EMD-30812
    Cryo-EM structure of Coxsackievirus B1 virion in complex with CAR
  120. EMD-30813
    EMD-30813
    Cryo-EM structure of Coxsackievirus B1 virion in complex with CAR at physiological temperature
  121. EMD-30814
    EMD-30814
    Cryo-EM structure of CAR triggered Coxsackievirus B1 A-particle
  122. EMD-30815
    EMD-30815
    Cryo-EM structure of Coxsackievirus B1 mature virion in complex with nAb 5F5
  123. EMD-30950
    EMD-30950
    SARS-CoV-2 spike in complex with the CA521 neutralizing antibody Fab (focused refinement on Fab-RBD)
  124. EMD-30951
    EMD-30951
    SARS-CoV-2 spike in complex with the CA521 neutralizing antibody Fab (consensus map)
  125. EMD-30990
    EMD-30990
    Cryo-EM structure of alpha 7 homo-tetradecamer
  126. EMD-30991
    EMD-30991
    Dislocated type of human proteasome alpha7 homo-tetradecamer
  127. EMD-30992
    EMD-30992
    Open type of human proteasome alpha 7 homo-tetradecamer
  128. EMD-31049
    EMD-31049
    Cryo-EM structure of human GABA(B) receptor-Gi protein complex
  129. EMD-31075
    EMD-31075
    p53-bound TFIID-based core PIC on HDM2 promoter
  130. EMD-31107
    EMD-31107
    TFIID-based core PIC on SCP promoter
  131. EMD-31108
    EMD-31108
    TFIID-based core PIC on PUMA promoter
  132. EMD-31109
    EMD-31109
    TFIID-based intermediate PIC on SCP promoter
  133. EMD-31110
    EMD-31110
    TFIID-based intermediate PIC on PUMA promoter
  134. EMD-31111
    EMD-31111
    TFIID-based holo PIC on SCP promoter
  135. EMD-31115
    EMD-31115
    TFIID lobe A subcomplex
  136. EMD-31116
    EMD-31116
    TFIID lobe B subcomplex
  137. EMD-31142
    EMD-31142
    Cryo-EM structure of human ABCB8 transporter in nucleotide binding state
  138. EMD-31177
    EMD-31177
    Structure of Machupo virus L polymerase in complex with Z protein and 3'-vRNA (dimeric complex)
  139. EMD-31178
    EMD-31178
    Structure of Lassa virus polymerase in complex with 3'-vRNA and Z mutant (F36A)
  140. EMD-31179
    EMD-31179
    Structure of Machupo virus L polymerase in complex with Z protein (dimeric form)
  141. EMD-31180
    EMD-31180
    Structure of monomeric complex of MACV L bound to Z and 3'-vRNA
  142. EMD-31191
    EMD-31191
    Human Mediator (deletion of MED1-IDR) in a Tail-extended conformation
  143. EMD-31192
    EMD-31192
    Human Mediator (deletion of MED1-IDR) Head module
  144. EMD-31193
    EMD-31193
    Human Mediator (deletion of MED1-IDR) Middle module
  145. EMD-31194
    EMD-31194
    Human Mediator (deletion of MED1-IDR) Tail module
  146. EMD-31195
    EMD-31195
    Structure of the human Mediator MED1 module
  147. EMD-31196
    EMD-31196
    Human Mediator (deletion of MED1-IDR) Head module near MED6