CryoEM structure of the spike S protein trimer of the omicron BA.1 variant prepared in the presence of compound II-Na salt

2026-05-06 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBe PDBe 2025-06-25 2026-05-06 2026-05-06 2026-05-06 Spanish Ministry of Science, Innovation, and Universities PID2020-120322RB-C21 Spain Spanish Ministry of Science, Innovation, and Universities PID2020-116880GB-I00 Spain CryoEM structure of the spike S protein trimer of the omicron BA.1 variant prepared in the presence of compound II-Na salt Llacer JL Lopez ML Spike, Omicron, SARS-CoV-2, VIRAL PROTEIN Marti-Mari O Moreno-Simoni M Aviles-Alia AI Rusu L Forcada-Nadal A Adhav A Lopez-Redondo ML Blazquez AB Esteban A Jimenez de Oya N Marina A Rubio V Llacer JL Gago F Martin-Acebes MA Perez-Perez MJ Geller R San-Felix A A Tetrapodal Tryptophan Derivative with Multiple Exposed Free Carboxylic Acids Blocks Host Cell Entry of Omicron SARS-Cov-2 and Respiratory Syncytial Virus. Acs Omega US 10 56830 56844 2025 41322621 doi:10.1021/acsomega.5c10442 2470-1343 EMDB EMD-54176 associated EM volume Spike from OMICRON_GSAS_2P BA.1 variant Spike from OMICRON_GSAS_2P BA.1 variant 0 1

SARS-CoV-2 Spike protein variant OMICRON with furin side replaced by GSAS and with 2 Proline substitution at 986 and 987

SARS-CoV-2 Spike from OMICRON_GSAS_2P BA.1 variant Severe acute respiratory syndrome coronavirus 2 Homo sapiens LEVO M F V F L V L L P L V S S Q C V N L T T R T Q L P P A Y T N S F T R G V Y Y P D K V F R S S V L H S T Q D L F L P F F S N V T W F H V I S G T N G T K R F D N P V L P F N D G V Y F A S I E K S N I I R G W I F G T T L D S K T Q S L L I V N N A T N V V I K V C E F Q F C N D P F L D H K N N K S W M E S E F R V Y S S A N N C T F E Y V S Q P F L M D L E G K Q G N F K N L R E F V F K N I D G Y F K I Y S K H T P I I V R E P E D L P Q G F S A L E P L V D L P I G I N I T R F Q T L L A L H R S Y L T P G D S S S G W T A G A A A Y Y V G Y L Q P R T F L L K Y N E N G T I T D A V D C A L D P L S E T K C T L K S F T V E K G I Y Q T S N F R V Q P T E S I V R F P N I T N L C P F D E V F N A T R F A S V Y A W N R K R I S N C V A D Y S V L Y N L A P F F T F K C Y G V S P T K L N D L C F T N V Y A D S F V I R G D E V R Q I A P G Q T G N I A D Y N Y K L P D D F T G C V I A W N S N K L D S K V S G N Y N Y L Y R L F R K S N L K P F E R D I S T E I Y Q A G N K P C N G V A G F N C Y F P L R S Y S F R P T Y G V G H Q P Y R V V V L S F E L L H A P A T V C G P K K S T N L V K N K C V N F N F N G L K G T G V L T E S N K K F L P F Q Q F G R D I A D T T D A V R D P Q T L E I L D I T P C S F G G V S V I T P G T N T S N Q V A V L Y Q G V N C T E V P V A I H A D Q L T P T W R V Y S T G S N V F Q T R A G C L I G A E Y V N N S Y E C D I P I G A G I C A S Y Q T Q T K S H G S A S S V A S Q S I I A Y T M S L G A E N S V A Y S N N S I A I P T N F T I S V T T E I L P V S M T K T S V D C T M Y I C G D S T E C S N L L L Q Y G S F C T Q L K R A L T G I A V E Q D K N T Q E V F A Q V K Q I Y K T P P I K Y F G G F N F S Q I L P D P S K P S K R S F I E D L L F N K V T L A D A G F I K Q Y G D C L G D I A A R D L I C A Q K F K G L T V L P P L L T D E M I A Q Y T S A L L A G T I T S G W T F G A G A A L Q I P F A M Q M A Y R F N G I G V T Q N V L Y E N Q K L I A N Q F N S A I G K I Q D S L S S T A S A L G K L Q D V V N H N A Q A L N T L V K Q L S S K F G A I S S V L N D I F S R L D P P E A E V Q I D R L I T G R L Q S L Q T Y V T Q Q L I R A A E I R A S A N L A A T K M S E C V L G Q S K R V D F C G K G Y H L M S F P Q S A P H G V V F L H V T Y V P A Q E K N F T T A P A I C H D G K A H F P R E G V F V S N G T H W F V T Q R N F Y E P Q I I T T D N T F V S G N C D V V I G I V N N T V Y D P L Q P E L D S F K E E L D K Y F K N H T S P D V D L G D I S G I N A S V V N I Q K E I D R L N E V A K N L N E S L I D L Q E L G K Y E Q P0DTC2 singleParticle particle 0.5 7.2 Quantifoil R1.2/1.3 GOLD 300 GLOW DISCHARGE 30 ETHANE 95 291.15 LEICA EM GP TFS GLACIOS OTHER BRIGHT FIELD FIELD EMISSION GUN 200 50.0 2.7 2.0 3.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON IV (4k x 4k) 1 5972 5.01 36.55 1 451475 PHASE FLIPPING AND AMPLITUDE CORRECTION C1 6.25 FSC 0.143 CUT-OFF Scipion 97694 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_54176.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 492 492 492 0 0 0 492 492 492 457.56 457.56 457.56 90.0 90.0 90.0 X Y Z -0.062271476 0.8515294 0.002518996 0.031966142 0.93 0.93 0.93 0.18 AUTHOR ::::EMDATABANK.org::::EMD-54176:::: emd_54176_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 492 492 492 0 0 0 492 492 492 457.56 457.56 457.56 90.0 90.0 90.0 X Y Z -0.0017257136 1.6316074 0.0010551166 0.022934213 0.93 0.93 0.93 AUTHOR ::::EMDATABANK.org::::EMD-54176:::: Sharpened map using DeepEMhancer emd_54176_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 492 492 492 0 0 0 492 492 492 457.56 457.56 457.56 90.0 90.0 90.0 X Y Z -0.23663083 1.0145568 0.0026625108 0.04044439 0.93 0.93 0.93 AUTHOR ::::EMDATABANK.org::::EMD-54176:::: emd_54176_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 492 492 492 0 0 0 492 492 492 457.56 457.56 457.56 90.0 90.0 90.0 X Y Z -0.24851772 1.0634608 0.0026397125 0.04041612 0.93 0.93 0.93 AUTHOR ::::EMDATABANK.org::::EMD-54176::::