2025-12-10
REL
PDBc
INITIAL_RELEASE
REPOSITORY
PDBj
PDBc
2024-12-17
2025-12-10
2025-12-10
2025-12-10
National Key Research and Development Program
2021YFC2302500
China
R&D Program of Guangzhou Laboratory
SRPG22-003
China
Structure of SARS-CoV-2 EG.5.1 Variant Spike protein complexed with antibody XGi-198
Qiu YN
Sun L
Spike-antibody complex, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex
Xie M
Qiu Y
Zhao X
Shi J
Liu Y
Zhang Q
He J
Li J
Liu L
Sun S
Zhu Y
Mao Q
Long Y
Oliveira TY
Wang Z
Zhou Y
Yan Y
Xia A
Zai W
Mayer CT
Xie Y
Jiang S
Lu L
Xia R
Wu F
Sun L
Wang P
Chu H
Wang Q
Orphan broadly RBD-binding antibodies annotate three remaining conserved RBD epitopes along SARS-CoV-2 evolution.
Nat Commun
UK
16
10566
10566
2025
41298374
doi:10.1038/s41467-025-65596-0
2041-1723
EMD-62744
consensus EM volume
EMD-62745
focused EM volume
EMD-62746
focused EM volume
EMD-62687
focused EM volume
9l2l
FULLOVERLAP
EMDB
EMD-62744
consensus EM volume
EMDB
EMD-62745
focused EM volume
EMDB
EMD-62746
focused EM volume
EMDB
EMD-62777
associated EM volume
Structure of SARS-CoV-2 EG.5.1 Variant Spike protein complexed with antibody XGi-
EMDB
EMD-62687
focused EM volume
PDB
9L05
unspecified
EG.5.1 spike protein (S) in complex with antibody XGi-198
EG.5.1 spike protein (S) in complex with antibody XGi-198
0
1
2
3
Severe acute respiratory syndrome coronavirus 2
XGi-198 heavy chain
1
2
Homo sapiens
XGi-198 light chain
1
3
Homo sapiens
EG.5.1 Spike glycoprotein
1
1
Severe acute respiratory syndrome coronavirus 2
Spike glycoprotein
Severe acute respiratory syndrome coronavirus 2
Omicron/EG.5.1
0.14314759400000002
6
Homo sapiens
LEVO
MPMGSLQPLATLYLLGMLVASVLAQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTHDLFLPFFSNVTWFHAIHVSG
TNGTKRFDNPALPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYQKNNKSWM
ESEFRVYSSANNCTFEYVSQPFLMDLEGKEGNFKNLREFVFKNIDGYFKIYSKHTPINLERDLPQGFSALEPLVDLPIGI
NITRFQTLLALHRSYLTPVDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIY
QTSNFRVQPTESIVRFPNITNLCPFHEVFNATTFASVYAWNRKRISNCVADYSVIYNFAPFFAFKCYGVSPTKLNDLCFT
NVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKPSGNYNYLYRLLRKSKLKPFERDISTEIY
QAGNKPCNGVAGPNCYSPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLT
ESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTW
RVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHGSASSVASQSIIAYTMSLGAENSVAYSNNSIA
IPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPP
IKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQY
TSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVN
HNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECV
LGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQ
IITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNL
NESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVFLSTFLSGLEVLFQGPGGWSHPQFEKGGGSGGGSGGSAWSHP
QFEKGGSHHHHHHHH
P0DTC2
XGi-198 heavy chain
Homo sapiens
0.049731945
6
Homo sapiens
LEVO
QVQLQESGPGLVRPSQTLSLTCTVSGGSVRNEYYYWSWIRQPPGQGLEWIGYMHNSGNTYYNPSLKSRVAISVDMSKNQF
SLKLSSVTVADTAVYYCARVDVGGTLVSTFDHWGQGILVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPV
TVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHTCPPCPAPEL
LGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWL
NGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTT
PPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK
XGi-198 light chain
Homo sapiens
0.023255407999999998
6
Homo sapiens
LEVO
EFMLTQPHSVSESPEMTVTISCTGSSGSIADNYVQWYQQRPGSAPTTVIYENYQRPSGVPNRFSGSIDSSSNSASLTISG
LKTEDEADYYCQSYDNSNVAVFGGGTQLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPV
KAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS
2-acetamido-2-deoxy-beta-D-glucopyranose
0.000221208
48
NAG
singleParticle
particle
8.0
ETHANE
TFS KRIOS
FLOOD BEAM
BRIGHT FIELD
FIELD EMISSION GUN
300
1.0
3.0
FEI FALCON IV (4k x 4k)
50.0
1
PHASE FLIPPING AND AMPLITUDE CORRECTION
C1
2.98
FSC 0.143 CUT-OFF
167476
PROJECTION MATCHING
PROJECTION MATCHING