2025-05-21
REL
RCSB
INITIAL_RELEASE
REPOSITORY
INITIAL_RELEASE
REPOSITORY
INITIAL_RELEASE
REPOSITORY
EXPERIMENTAL_SUMMARY
em_admin
em_software
- _em_admin.last_update
- _em_software.name
COORDINATE_REPLACEMENT
AUTHOR
Polymer geometry
REFINEMENT_DESCRIPTION
atom_site
atom_site_anisotrop
em_software
pdbx_entity_branch_descriptor
pdbx_struct_sheet_hbond
pdbx_validate_close_contact
pdbx_validate_peptide_omega
pdbx_validate_rmsd_angle
pdbx_validate_torsion
refine_ls_restr
software
struct_conf
struct_conn
struct_mon_prot_cis
struct_sheet
struct_sheet_order
struct_sheet_range
- _atom_site.B_iso_or_equiv
- _atom_site.Cartn_x
- _atom_site.Cartn_y
- _atom_site.Cartn_z
- _atom_site_anisotrop.U[1][1]
- _atom_site_anisotrop.U[2][2]
- _atom_site_anisotrop.U[3][3]
- _em_software.category
- _em_software.fitting_id
- _em_software.imaging_id
- _pdbx_entity_branch_descriptor.descriptor
- _pdbx_validate_close_contact.auth_asym_id_1
- _pdbx_validate_close_contact.auth_asym_id_2
- _pdbx_validate_close_contact.auth_atom_id_1
- _pdbx_validate_close_contact.auth_atom_id_2
- _pdbx_validate_close_contact.auth_comp_id_1
- _pdbx_validate_close_contact.auth_comp_id_2
- _pdbx_validate_close_contact.auth_seq_id_1
- _pdbx_validate_close_contact.auth_seq_id_2
- _pdbx_validate_close_contact.dist
- _pdbx_validate_peptide_omega.auth_asym_id_1
- _pdbx_validate_peptide_omega.auth_asym_id_2
- _pdbx_validate_peptide_omega.auth_comp_id_1
- _pdbx_validate_peptide_omega.auth_seq_id_1
- _pdbx_validate_peptide_omega.auth_seq_id_2
- _pdbx_validate_peptide_omega.omega
- _refine_ls_restr.dev_ideal
- _software.version
- _struct_conn.pdbx_dist_value
- _struct_sheet.number_strands
DATABASE_REFERENCES
citation
citation_author
database_2
- _database_2.pdbx_DOI
- _database_2.pdbx_database_accession
STRUCTURE_SUMMARY
chem_comp_atom
chem_comp_bond
citation
em_admin
pdbx_entry_details
pdbx_modification_feature
- _citation.journal_id_ISSN
- _em_admin.last_update
- _pdbx_entry_details.has_protein_modification
DATA_COLLECTION
em_admin
em_software
- _em_admin.last_update
- _em_software.name
RCSB
RCSB
2021-04-24
2021-05-12
2021-05-12
2025-05-21
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
75N93019C00062
United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
HHSN272201700060C
United States
SARS-CoV-2 Spike in complex with neutralizing Fab SARS2-38 (three down conformation)
Adams LJ
Fremont DH
Glycoprotein, Antibody, VIRAL PROTEIN-IMMUNE SYSTEM complex, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID
VanBlargan LA
Adams LJ
Liu Z
Chen RE
Gilchuk P
Raju S
Smith BK
Zhao H
Case JB
Winkler ES
Whitener BM
Droit L
Aziati ID
Bricker TL
Joshi A
Shi PY
Creanga A
Pegu A
Handley SA
Wang D
Boon ACM
Crowe Jr JE
Whelan SPJ
Fremont DH
Diamond MS
A potently neutralizing SARS-CoV-2 antibody inhibits variants of concern by utilizing unique binding residues in a highly conserved epitope.
Immunity
US
54
2399
2416.e6
2021
34481543
doi:10.1016/j.immuni.2021.08.016
1074-7613
2048
IUNIEH
VanBlargan L
Adams L
Liu Z
Chen RE
Gilchuk P
Raju S
Smith B
Zhao H
Case JB
Winkler ES
Whitener B
Droit L
Aziati I
Shi PY
Creanga A
Pegu A
Handley S
Wang D
Boon A
Crowe JE
Whelan SPJ
Fremont D
Diamond M
A potently neutralizing anti-SARS-CoV-2 antibody inhibits variants of concern by binding a highly conserved epitope.
Biorxiv
US
2021
33907753
doi:10.1101/2021.04.26.441501
2692-8205
EMD-23899
other EM volume
7mkl
FULLOVERLAP
SARS-CoV-2 spike bound by SARS2-38 antibody Fab
SARS-CoV-2 spike bound by SARS2-38 antibody Fab
0
1
2
3
Severe acute respiratory syndrome coronavirus 2
Spike glycoprotein
Severe acute respiratory syndrome coronavirus 2
0.12415253899999999
3
Homo sapiens
LEVO
AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIF
GTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNF
KNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYY
VGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATR
FASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLP
DDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQ
PYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILD
ITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPI
GAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDS
TECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKV
TLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRF
NGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDP
PEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVT
YVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELD
S
P0DTC2
SARS2-38 Fv heavy chain
Mus musculus
0.012490881999999998
1
LEVO
QVQLKESGPGLVAPSQSLSITCTVSGFSLTRYGVHWVRQPPGKGLEWLGVIWADGSTYYNSALMSRLSISKDNSKSQVFL
NMNSLQTDDTAKYYCARDGRGYDDYWGQGTTLT
SARS2-38 Fv light chain
Mus musculus
0.011419786999999999
1
LEVO
QIVLTQSPAIMSASPGEKVTMTCSASSTVSFIYWYQQKPGSSPRLLIYDTSNPASGVPVRFSGSGCGTSYYLTISRMEAE
DAATYYCQQWNTYPLTFGAGTKLEL
2-acetamido-2-deoxy-beta-D-glucopyranose
0.000221208
33
NAG
singleParticle
particle
7.4
ETHANE
FEI TITAN KRIOS
FLOOD BEAM
BRIGHT FIELD
FIELD EMISSION GUN
300
FEI FALCON IV (4k x 4k)
50.0
1
PHASE FLIPPING AND AMPLITUDE CORRECTION
3.2
FSC 0.143 CUT-OFF
cryoSPARC
3.1.0
272007
MAXIMUM LIKELIHOOD
MAXIMUM LIKELIHOOD