2025-10-15 REL RCSB INITIAL_RELEASE REPOSITORY RCSB RCSB 2024-12-31 2025-10-15 2025-10-15 2025-10-15 National Institutes of Health/National Cancer Institute (NIH/NCI) R01 CA262188 United States National Institutes of Health/National Cancer Institute (NIH/NCI) R01 CA233800 United States National Institutes of Health/National Cancer Institute (NIH/NCI) 5F31 CA281197 United States Cryo-EM structure of p47 bound to VCP N-domain (with D1 domain) Shah B Hunkeler M Buhrlage SJ Fischer EF double-ring hexameric complex, valosin containing protein, ATPase, VCP, mammalian, p97, p47, adapter, SHP, UBX, HYDROLASE Shah B Hunkeler M Bratt A Yue H Jaen Maisonet I Fischer ES Buhrlage SJ Structural basis of VCP-VCPIP1-p47 ternary complex in Golgi maintenance. Nat Commun UK 16 8025 8025 2025 40877265 doi:10.1038/s41467-025-63161-3 2041-1723 9mpu FULLOVERLAP PDB 9MPQ unspecified
D_1000288691
 PDB 9MPR unspecified
D_1000288718
 PDB 9MPS unspecified
D_1000288721
 PDB 9MPT unspecified
D_1000288722
 EMDB EMD-48505 associated EM volume
Cryo-EM structure of p47 bound to VCP N-domain (with D1 domain)
 Complex of valosin containing protein (VCP)/p97 bound to valosin containing protein interacting protein 1 (VCPIP1) and p47 Complex of valosin containing protein (VCP)/p97 bound to valosin containing protein interacting protein 1 (VCPIP1) and p47 0 1 2
Full length valosin containing protein (VCP)/p97 with full length valosin containing protein interacting protein 1 (VCPIP1) and p47
Homo sapiens Valosin containing protein (VCP) 1 2 Homo sapiens p47 1 1
Adapter of valosin containing protein (VCP)/p97
 NSFL1 cofactor p47 Homo sapiens 0.043535906
N-term His tagged p47
1 Escherichia coli LEVO MHHHHHHHHHHDLGTENLYFQSMMAAERQEALREFVAVTGAEEDRARFFLESAGWDLQIALASFYEDGGDEDIVTISQAT PSSVSRGTAPSDNRVTSFRDLIHDQDEDEEEEEGQRFYAGGSERSGQQIVGPPRKKSPNELVDDLFKGAKEHGAVAVERV TKSPGETSKPRPFAGGGYRLGAAPEEESAYVAGEKRQHSSQDVHVVLKLWKSGFSLDNGELRSYQDPSNAQFLESIRRGE VPAELRRLAHGGQVNLDMEDHRDEDFVKPKGAFKAFTGEGQKLGSTAPQVLSTSSPAQQAENEAKASSSILIDESEPTTN IQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFILMTTFPNKELADESQTLKEANLLNAVIVQRLT Q9UNZ2 Transitional endoplasmic reticulum ATPase Homo sapiens 0.092022539
N-term FLAG-tagged VCP
1 Homo sapiens LEVO MGDYKDDDDKGGGSGGLEVLFQGPGSMASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRG DTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVY LKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCRKQLA QIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAE KNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDA TGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRW ALSQSNPSALRETVVEVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANE CQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTK KNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRA CKLAIRESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTLQQSRGFGSFRFP SGNQGGAGPSQGSGGGTGGSVYTEDNDDDLYG P55072 3.6.4.6 singleParticle particle 2 7.4 30.0 HEPES 150.0 NaCl sodium chloride 3.0 TCEP Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY GLOW DISCHARGE AIR 0.039 ETHANE 90 283.15 LEICA EM GP
Final concentration of 0.2 mM CHAPSO
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.8 2.2 165000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 10 FEI FALCON IV (4k x 4k) 1 12261 2.87 49.22 1 2003371 cryoSPARC 4.60 PHASE FLIPPING AND AMPLITUDE CORRECTION FOURIER SPACE 4.0 FSC 0.143 CUT-OFF cryoSPARC 4.6.0 54855 MAXIMUM LIKELIHOOD cryoSPARC 4.60 MAXIMUM LIKELIHOOD cryoSPARC 4.6.0 emd_48505.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 180 180 180 0 0 0 180 180 180 353.28 353.28 353.28 90.0 90.0 90.0 X Y Z -0.6068542 1.0354465 -0.0011220628 0.024708107 1.9626666 1.9626666 1.9626666 0.187 AUTHOR 5FTK PDB experimental model REAL emd_48505_msk_1.map emd_48505_msk_2.map emd_48505_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 180 180 180 0 0 0 180 180 180 353.28 353.28 353.28 90.0 90.0 90.0 X Y Z -0.8922245 1.6432648 -0.0011220628 0.032132965 1.9626666 1.9626666 1.9626666 AUTHOR emd_48505_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 180 180 180 0 0 0 180 180 180 353.28 353.28 353.28 90.0 90.0 90.0 X Y Z -0.90235406 1.4772657 0.0011784992 0.045915138 1.9626666 1.9626666 1.9626666 AUTHOR Half-map A emd_48505_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 180 180 180 0 0 0 180 180 180 353.28 353.28 353.28 90.0 90.0 90.0 X Y Z -0.9914577 1.5434028 0.0011881848 0.046209957 1.9626666 1.9626666 1.9626666 AUTHOR Half-map B