PDB entry 7my3

View 7my3 on RCSB PDB site
Description: CryoEM structure of neutralizing nanobody Nb12 in complex with SARS-CoV2 spike
Class: immune system/viral protein
Keywords: SARS-CoV2, nanobody, neutralizing, spike, IMMUNE SYSTEM-VIRAL PROTEIN complex
Deposited on 2021-05-20, released 2021-06-16
The last revision prior to the SCOPe 2.08 freeze date was dated 2021-07-28, with a file datestamp of 2021-07-23.
Experiment type: EM
Resolution: 2.9 Å
R-factor: N/A
AEROSPACI score: 0.21 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Spike glycoprotein
    Species: Severe acute respiratory syndrome coronavirus 2 [TaxId:2697049]
    Gene: S, 2
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0DTC2 (0-1207)
      • engineered mutation (681-682)
      • engineered mutation (684)
      • engineered mutation (816)
      • engineered mutation (891)
      • engineered mutation (898)
      • engineered mutation (941)
      • engineered mutation (985-986)
      • expression tag (1208-1287)
  • Chain 'B':
    Compound: Spike glycoprotein
    Species: Severe acute respiratory syndrome coronavirus 2 [TaxId:2697049]
    Gene: S, 2
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0DTC2 (0-1207)
      • engineered mutation (681-682)
      • engineered mutation (684)
      • engineered mutation (816)
      • engineered mutation (891)
      • engineered mutation (898)
      • engineered mutation (941)
      • engineered mutation (985-986)
      • expression tag (1208-1287)
  • Chain 'C':
    Compound: Spike glycoprotein
    Species: Severe acute respiratory syndrome coronavirus 2 [TaxId:2697049]
    Gene: S, 2
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0DTC2 (0-1207)
      • engineered mutation (681-682)
      • engineered mutation (684)
      • engineered mutation (816)
      • engineered mutation (891)
      • engineered mutation (898)
      • engineered mutation (941)
      • engineered mutation (985-986)
      • expression tag (1208-1287)
  • Chain 'D':
    Compound: Nanobody Nb12
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 7MY3 (0-126)
    Domains in SCOPe 2.08: d7my3d1, d7my3d2
  • Chain 'E':
    Compound: Nanobody Nb12
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 7MY3 (0-126)
    Domains in SCOPe 2.08: d7my3e1, d7my3e2
  • Chain 'H':
    Compound: Nanobody Nb12
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 7MY3 (0-126)
    Domains in SCOPe 2.08: d7my3h1, d7my3h2
  • Heterogens: NAG

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >7my3D (D:)
qvkleesgggsvqaggslrlictapglthnncgldwyrrapgkerefvssisadgttsya
dsvkgrftiskdkvedtvylqmnslkpedtaiyscktafpyfgnscvldywgqgtsvtvs
shhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >7my3D (D:)
qvkleesgggsvqaggslrlictapglthnncgldwyrrapgkerefvssisadgttsya
dsvkgrftiskdkvedtvylqmnslkpedtaiyscktafpyfgnscvldywgqgtsvtvs

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >7my3E (E:)
qvkleesgggsvqaggslrlictapglthnncgldwyrrapgkerefvssisadgttsya
dsvkgrftiskdkvedtvylqmnslkpedtaiyscktafpyfgnscvldywgqgtsvtvs
shhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >7my3E (E:)
qvkleesgggsvqaggslrlictapglthnncgldwyrrapgkerefvssisadgttsya
dsvkgrftiskdkvedtvylqmnslkpedtaiyscktafpyfgnscvldywgqgtsvtvs

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >7my3H (H:)
qvkleesgggsvqaggslrlictapglthnncgldwyrrapgkerefvssisadgttsya
dsvkgrftiskdkvedtvylqmnslkpedtaiyscktafpyfgnscvldywgqgtsvtvs
shhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >7my3H (H:)
qvkleesgggsvqaggslrlictapglthnncgldwyrrapgkerefvssisadgttsya
dsvkgrftiskdkvedtvylqmnslkpedtaiyscktafpyfgnscvldywgqgtsvtvs