9COO: Nanobody 4
Nanobody 4 bound to Apolipoprotein B 100. Determined by electron microscopy at 3.73 Å resolution. Released 25 Dec 2024.
- Method
- Electron microscopy
- Resolution
- 3.73 Å
- Organisms
- Homo sapiens, Escherichia coli, Mus musculus
- Chains
- 6
- Atoms
- 7,493
- Mol. weight
- 728.18 kDa
- Ligands
- CA, NAG
- Released
- 25 Dec 2024
Explore 9COO in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9COO contains 15 α-helices and 81 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 1 helix, 39 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2822 | 1 | 1 |
| β-strand | 2825-2831 | 7 | 1 |
| β-strand | 2835-2846 | 12 | 1 |
| β-strand | 2849-2862 | 14 | 1 |
| β-strand | 2865-2877 | 13 | 1 |
| β-strand | 2882-2895 | 14 | 1 |
| β-strand | 2900-2915 | 16 | 1 |
| β-strand | 2918-2922 | 5 | 1 |
| β-strand | 2925-2932 | 8 | 1 |
| β-strand | 2939-2951 | 13 | 1 |
| β-strand | 2954-2962 | 9 | 1 |
| β-strand | 2964 | 1 | 1 |
| β-strand | 2968-2975 | 8 | 1 |
| β-strand | 2978-2979 | 2 | 1 |
| β-strand | 2983-2994 | 12 | 1 |
| β-strand | 3000-3009 | 10 | 1 |
| β-strand | 3015-3023 | 9 | 1 |
| β-strand | 3025-3026 | 2 | 1 |
| β-strand | 3030-3031 | 2 | 1 |
| β-strand | 3034-3037 | 4 | 1 |
| β-strand | 3040-3041 | 2 | 1 |
| β-strand | 3042 | 1 | 2 |
| β-strand | 3045 | 1 | 2 |
| β-strand | 3052-3060 | 9 | 1 |
| β-strand | 3064-3074 | 11 | 1 |
| β-strand | 3077 | 1 | 3 |
| β-strand | 3084 | 1 | 3 |
| β-strand | 3085-3093 | 9 | 1 |
| β-strand | 3096-3104 | 9 | 1 |
| β-strand | 3114-3122 | 9 | 1 |
| α-helix | 3153-3156 | 4 | |
| β-strand | 3166-3168 | 3 | 1 |
| β-strand | 3173-3174 | 2 | 1 |
| β-strand | 3337-3344 | 8 | 1 |
| β-strand | 3349-3356 | 8 | 1 |
| β-strand | 3364-3367 | 4 | 1 |
| β-strand | 3368 | 1 | 4 |
| β-strand | 3381 | 1 | 4 |
| β-strand | 3382-3386 | 5 | 1 |
| β-strand | 3394-3398 | 5 | 1 |
Chain B: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 336-352 | 17 | |
| α-helix | 358-369 | 12 | |
| α-helix | 375-387 | 13 | |
| α-helix | 392-405 | 14 | |
| α-helix | 419-427 | 9 | |
| α-helix | 435-447 | 13 | |
| α-helix | 452-468 | 17 | |
Chain H: 0 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 5 |
| β-strand | 12 | 1 | 6 |
| β-strand | 18-25 | 8 | 5 |
| β-strand | 33-39 | 7 | 7 |
| β-strand | 46-51 | 6 | 7 |
| β-strand | 60 | 1 | 7 |
| β-strand | 68-73 | 6 | 5 |
| β-strand | 78-83 | 6 | 5 |
| β-strand | 92-99 | 8 | 7 |
| β-strand | 117-119 | 3 | 7 |
| β-strand | 121 | 1 | 6 |
Chain L: 2 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-6 | 3 | 8 |
| β-strand | 10 | 1 | 9 |
| β-strand | 19-25 | 7 | 8 |
| β-strand | 30 | 1 | 10 |
| β-strand | 37 | 1 | 10 |
| β-strand | 39-44 | 6 | 9 |
| α-helix | 49-50 | 2 | |
| β-strand | 51-55 | 5 | 9 |
| β-strand | 59-60 | 2 | 9 |
| β-strand | 68-73 | 6 | 8 |
| β-strand | 76-81 | 6 | 8 |
| α-helix | 86-88 | 3 | |
| β-strand | 91-96 | 6 | 9 |
| β-strand | 102-103 | 2 | 9 |
| β-strand | 107-108 | 2 | 9 |
Chain N: 2 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-7 | 2 | 11 |
| β-strand | 10-13 | 4 | 12 |
| β-strand | 17-23 | 7 | 11 |
| β-strand | 33-39 | 7 | 12 |
| β-strand | 46-51 | 6 | 12 |
| β-strand | 58-60 | 3 | 12 |
| β-strand | 68-73 | 6 | 11 |
| β-strand | 78-84 | 7 | 11 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-99 | 8 | 12 |
| α-helix | 114-116 | 3 | |
| β-strand | 117-122 | 6 | 12 |
Chain R: 3 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 72-74 | 3 | 13 |
| β-strand | 82-84 | 3 | 13 |
| α-helix | 85-87 | 3 | |
| β-strand | 113-115 | 3 | 14 |
| β-strand | 121-123 | 3 | 14 |
| α-helix | 138-141 | 4 | |
| β-strand | 152-154 | 3 | 15 |
| β-strand | 160-162 | 3 | 15 |
| β-strand | 166 | 1 | 16 |
| β-strand | 171 | 1 | 16 |
| α-helix | 185-188 | 4 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Apolipoprotein B 100 | A | protein | 4563 | Homo sapiens | P04114 |
| Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G | B | protein | 545 | Escherichia coli | P02976 (AlphaFold model), P06654 (AlphaFold model), P0AEX9 (AlphaFold model) |
| Legobody 8D3 Fab Heavy Chain | H | protein | 234 | Mus musculus | |
| Legobody 8D3 Fab Light Chain | L | protein | 219 | Mus musculus | |
| ApoB100 nanobody 4 | N | protein | 131 | Camelus bactrianus | |
| Low-density lipoprotein receptor | R | protein | 795 | Homo sapiens | P01130 |
Sequence of entity 1 (A), FASTA
>9COO_1 Apolipoprotein B 100 (chains A)
MDPPRPALLALLALPALLLLLLAGARAEEEMLENVSLVCPKDATRFKHLRKYTYNYEAES
SSGVPGTADSRSATRINCKVELEVPQLCSFILKTSQCTLKEVYGFNPEGKALLKKTKNSE
EFAAAMSRYELKLAIPEGKQVFLYPEKDEPTYILNIKRGIISALLVPPETEEAKQVLFLD
TVYGNCSTHFTVKTRKGNVATEISTERDLGQCDRFKPIRTGISPLALIKGMTRPLSTLIS
SSQSCQYTLDAKRKHVAEAICKEQHLFLPFSYKNKYGMVAQVTQTLKLEDTPKINSRFFG
EGTKKMGLAFESTKSTSPPKQAEAVLKTLQELKKLTISEQNIQRANLFNKLVTELRGLSD
EAVTSLLPQLIEVSSPITLQALVQCGQPQCSTHILQWLKRVHANPLLIDVVTYLVALIPE
PSAQQLREIFNMARDQRSRATLYALSHAVNNYHKTNPTGTQELLDIANYLMEQIQDDCTG
DEDYTYLILRVIGNMGQTMEQLTPELKSSILKCVQSTKPSLMIQKAAIQALRKMEPKDKD
QEVLLQTFLDDASPGDKRLAAYLMLMRSPSQADINKIVQILPWEQNEQVKNFVASHIANI
LNSEELDIQDLKKLVKEALKESQLPTVMDFRKFSRNYQLYKSVSLPSLDPASAKIEGNLI
FDPNNYLPKESMLKTTLTAFGFASADLIEIGLEGKGFEPTLEALFGKQGFFPDSVNKALY
WVNGQVPDGVSKVLVDHFGYTKDDKHEQDMVNGIMLSVEKLIKDLKSKEVPEARAYLRIL
GEELGFASLHDLQLLGKLLLMGARTLQGIPQMIGEVIRKGSKNDFFLHYIFMENAFELPT
GAGLQLQISSSGVIAPGAKAGVKLEVANMQAELVAKPSVSVEFVTNMGIIIPDFARSGVQ
MNTNFFHESGLEAHVALKAGKLKFIIPSPKRPVKLLSGGNTLHLVSTTKTEVIPPLIENR
QSWSVCKQVFPGLNYCTSGAYSNASSTDSASYYPLTGDTRLELELRPTGEIEQYSVSATY
ELQREDRALVDTLKFVTQAEGAKQTEATMTFKYNRQSMTLSSEVQIPDFDVDLGTILRVN
DESTEGKTSYRLTLDIQNKKITEVALMGHLSCDTKEERKIKGVISIPRLQAEARSEILAH
WSPAKLLLQMDSSATAYGSTVSKRVAWHYDEEKIEFEWNTGTNVDTKKMTSNFPVDLSDY
PKSLHMYANRLLDHRVPQTDMTFRHVGSKLIVAMSSWLQKASGSLPYTQTLQDHLNSLKE
FNLQNMGLPDFHIPENLFLKSDGRVKYTLNKNSLKIEIPLPFGGKSSRDLKMLETVRTPA
LHFKSVGFHLPSREFQVPTFTIPKLYQLQVPLLGVLDLSTNVYSNLYNWSASYSGGNTST
DHFSLRARYHMKADSVVDLLSYNVQGSGETTYDHKNTFTLSCDGSLRHKFLDSNIKFSHV
EKLGNNPVSKGLLIFDASSSWGPQMSASVHLDSKKKQHLFVKEVKIDGQFRVSSFYAKGT
YGLSCQRDPNTGRLNGESNLRFNSSYLQGTNQITGRYEDGTLSLTSTSDLQSGIIKNTAS
LKYENYELTLKSDTNGKYKNFATSNKMDMTFSKQNALLRSEYQADYESLRFFSLLSGSLN
SHGLELNADILGTDKINSGAHKATLRIGQDGISTSATTNLKCSLLVLENELNAELGLSGA
SMKLTTNGRFREHNAKFSLDGKAALTELSLGSAYQAMILGVDSKNIFNFKVSQEGLKLSN
DMMGSYAEMKFDHTNSLNIAGLSLDFSSKLDNIYSSDKFYKQTVNLQLQPYSLVTTLNSD
LKYNALDLTNNGKLRLEPLKLHVAGNLKGAYQNNEIKHIYAISSAALSASYKADTVAKVQ
GVEFSHRLNTDIAGLASAIDMSTNYNSDSLHFSNVFRSVMAPFTMTIDAHTNGNGKLALW
GEHTGQLYSKFLLKAEPLAFTFSHDYKGSTSHHLVSRKSISAALEHKVSALLTPAEQTGT
WKLKTQFNNNEYSQDLDAYNTKDKIGVELTGRTLADLTLLDSPIKVPLLLSEPINIIDAL
EMRDAVEKPQEFTIVAFVKYDKNQDVHSINLPFFETLQEYFERNRQTIIVVLENVQRNLK
HINIDQFVRKYRAALGKLPQQANDYLNSFNWERQVSHAKEKLTALTKKYRITENDIQIAL
DDAKINFNEKLSQLQTYMIQFDQYIKDSYDLHDLKIAIANIIDEIIEKLKSLDEHYHIRV
NLVKTIHDLHLFIENIDFNKSGSSTASWIQNVDTKYQIRIQIQEKLQQLKRHIQNIDIQH
LAGKLKQHIEAIDVRVLLDQLGTTISFERINDILEHVKHFVINLIGDFEVAEKINAFRAK
VHELIERYEVDQQIQVLMDKLVELAHQYKLKETIQKLSNVLQQVKIKDYFEKLVGFIDDA
VKKLNELSFKTFIEDVNKFLDMLIKKLKSFDYHQFVDETNDKIREVTQRLNGEIQALELP
QKAEALKLFLEETKATVAVYLESLQDTKITLIINWLQEALSSASLAHMKAKFRETLEDTR
DRMYQMDIQQELQRYLSLVGQVYSTLVTYISDWWTLAAKNLTDFAEQYSIQDWAKRMKAL
VEQGFTVPEIKTILGTMPAFEVSLQALQKATFQTPDFIVPLTDLRIPSVQINFKDLKNIK
IPSRFSTPEFTILNTFHIPSFTIDFVEMKVKIIRTIDQMLNSELQWPVPDIYLRDLKVED
IPLARITLPDFRLPEIAIPEFIIPTLNLNDFQVPDLHIPEFQLPHISHTIEVPTFGKLYS
ILKIQSPLFTLDANADIGNGTTSANEAGIAASITAKGESKLEVLNFDFQANAQLSNPKIN
PLALKESVKFSSKYLRTEHGSEMLFFGNAIEGKSNTVASLHTEKNTLELSNGVIVKINNQ
LTLDSNTKYFHKLNIPKLDFSSQADLRNEIKTLLKAGHIAWTSSGKGSWKWACPRFSDEG
THESQISFTIEGPLTSFGLSNKINSKHLRVNQNLVYESGSLNFSKLEIQSQVDSQHVGHS
VLTAKGMALFGEGKAEFTGRHDAHLNGKVIGTLKNSLFFSAQPFEITASTNNEGNLKVRF
PLRLTGKIDFLNNYALFLSPSAQQASWQVSARFNQYKYNQNFSAGNNENIMEAHVGINGE
ANLDFLNIPLTIPEMRLPYTIITTPPLKDFSLWEKTGLKEFLKTTKQSFDLSVKAQYKKN
KHRHSITNPLAVLCEFISQSIKSFDRHFEKNRNNALDFVTKSYNETKIKFDKYKAEKSHD
ELPRTFQIPGYTVPVVNVEVSPFTIEMSAFGYVFPKAVSMPSFSILGSDVRVPSYTLILP
SLELPVLHVPRNLKLSLPDFKELCTISHIFIPAMGNITYDFSFKSSVITLNTNAELFNQS
DIVAHLLSSSSSVIDALQYKLEGTTRLTRKRGLKLATALSLSNKFVEGSHNSTVSLTTKN
MEVSVATTTKAQIPILRMNFKQELNGNTKSKPTVSSSMEFKYDFNSSMLYSTAKGAVDHK
LSLESLTSYFSIESSTKGDVKGSVLSREYSGTIASEANTYLNSKSTRSSVKLQGTSKIDD
IWNLEVKENFAGEATLQRIYSLWEHSTKNHLQLEGLFFTNGEHTSKATLELSPWQMSALV
QVHASQPSSFHDFPDLGQEVALNANTKNQKIRWKNEVRIHSGSFQSQVELSNDQEKAHLD
IAGSLEGHLRFLKNIILPVYDKSLWDFLKLDVTTSIGRRQHLRVSTAFVYTKNPNGYSFS
IPVKVLADKFIIPGLKLNDLNSVLVMPTFHVPFTDLQVPSCKLDFREIQIYKKLRTSSFA
LNLPTLPEVKFPEVDVLTKYSQPEDSLIPFFEITVPESQLTVSQFTLPKSVSDGIAALDL
NAVANKIADFELPTIIVPEQTIEIPSIKFSVPAGIVIPSFQALTARFEVDSPVYNATWSA
SLKNKADYVETVLDSTCSSTVQFLEYELNVLGTHKIEDGTLASKTKGTFAHRDFSAEYEE
DGKYEGLQEWEGKAHLNIKSPAFTDLHLRYQKDKKGISTSAASPAVGTVGMDMDEDDDFS
KWNFYYSPQSSPDKKLTIFKTELRVRESDEETQIKVNWEEEAASGLLTSLKDNVPKATGV
LYDYVNKYHWEHTGLTLREVSSKLRRNLQNNAEWVYQGAIRQIDDIDVRFQKAASGTTGT
YQEWKDKAQNLYQELLTQEGQASFQGLKDNVFDGLVRVTQEFHMKVKHLIDSLIDFLNFP
RFQFPGKPGIYTREELCTMFIREVGTVLSQVYSKVHNGSEILFSYFQDLVITLPFELRKH
KLIDVISMYRELLKDLSKEAQEVFKAIQSLKTTEVLRNLQDLLQFIFQLIEDNIKQLKEM
KFTYLINYIQDEINTIFSDYIPYVFKLLKENLCLNLHKFNEFIQNELQEASQELQQIHQY
IMALREEYFDPSIVGWTVKYYELEEKIVSLIKNLLVALKDFHSEYIVSASNFTSQLSSQV
EQFLHRNIQEYLSILTDPDGKGKEKIAELSATAQEIIKSQAIATKKIISDYHQQFRYKLQ
DFSDQLSDYYEKFIAESKRLIDLSIQNYHTFLIYITELLKKLQSTTVMNPYMKLAPGELT
IIL
Sequence of entity 2 (B), FASTA
>9COO_2 Maltodextrin-binding protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G (chains B)
MKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDI
IFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNK
DLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIK
DVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSK
VNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPL
GAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDQ
ALAFAQILIMPNLTEEQRNGFIQSLKDDPSVSKEILAEAKKLNEHQAPKGGSGGAGSGDQ
QSAFYEILNMPNLNEAQRNGFIQSLKDDPSQSTNVLGEAKKLNESQAGGGSGGGSGGSAV
TTYKLVINGKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTEGSGH
HHHHH
Sequence of entity 3 (H), FASTA
>9COO_3 Legobody 8D3 Fab Heavy Chain (chains H)
DVQLVESGGGLVQPGKSLRLSCAASGFTFSNFGMHWVRQAPEMGLEWVAYISSGSTTKYY
GDTVKGRFTISRDNPKNTLYLQMNSLRSEDTAMYYCARRPLYDGDYGYPMDYWGQGTSVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGSHHHHHH
Sequence of entity 4 (L), FASTA
>9COO_4 Legobody 8D3 Fab Light Chain (chains L)
NIMLTQSPSSLAVSAGERVTMSCKSTQSILYNSNQKTYLAWYQQKPGQSPKLLIYWASTR
ASGVPDRFTGSGSGTDFTLTINSVQPEDLAVYYCHQYLSAWTFGGGTKLEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
Sequence of entity 5 (N), FASTA
>9COO_5 ApoB100 nanobody 4 (chains N)
QVQLQESGGGLVQAGGSLRLSCVASGYTDGAVNMGWFRQAPGKDRDWVAAISPGGGLTYY
ADSVKGRFTISQDKAKNTVYLQMNSLKPEDTAIYYCAAARSLAHFKLSQYNYWGQGTQVT
VSSLEHHHHHH
Sequence of entity 6 (R), FASTA
>9COO_6 Low-density lipoprotein receptor (chains R)
VTCKSGDFSCGGRVNRCIPQFWRCDGQVDCDNGSDEQGCPPKTCSQDEFRCHDGKCISRQ
FVCDSDRDCLDGSDEASCPVLTCGPASFQCNSSTCIPQLWACDNDPDCEDGSDEWPQRCR
GLYVFQGDSSPCSAFEFHCLSGECIHSSWRCDGGPDCKDKSDEENCAVATCRPDEFQCSD
GNCIHGSRQCDREYDCKDMSDEVGCVNVTLCEGPNKFKCHSGECITLDKVCNMARDCRDW
SDEPIKECGTNECLDNNGGCSHVCNDLKIGYECLCPDGFQLVAQRRCEDIDECQDPDTCS
QLCVNLEGGYKCQCEEGFQLDPHTKACKAVGSIAYLFFTNRHEVRKMTLDRSEYTSLIPN
LRNVVALDTEVASNRIYWSDLSQRMICSTQLDRAHGVSSYDTVISRDIQAPDGLAVDWIH
SNIYWTDSVLGTVSVADTKGVKRKTLFRENGSKPRAIVVDPVHGFMYWTDWGTPAKIKKG
GLNGVDIYSLVTENIQWPNGITLDLLSGRLYWVDSKLHSISSIDVNGGNRKTILEDEKRL
AHPFSLAVFEDKVFWTDIINEAIFSANRLTGSDVNLLAENLLSPEDMVLFHNLTQPRGVN
WCERTTLSNGGCQYLCLPAPQINPHSPKFTCACPDGMLLARDMRSCLTEAEAAVATQETS
TVRLKVSSTAVRTQHTTTRPVPDTSRLPGATPGLTTVEIVTMSHQALGDVAGRGNEKKPS
SVRALSIVLPIVLLVFLCLGVFLLWKNWRLKNINSINFDNPVYQKTTEDEVHICHNQDGY
SYPSRQMVSLEDDVA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CA | Calcium ion | Ca | 3 |
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 3 |
Primary citation
Structure of apolipoprotein B100 bound to the low-density lipoprotein receptor. Reimund, M., Dearborn, A.D., Graziano, G. et al. Nature (2025) 638:829-835. DOI 10.1038/s41586-024-08223-0 · PubMed
Other PDB entries of the same protein (UniProt P04114), best resolution first:
- 9BDE 4.18 Å, Middle Region of Apolipoprotein B 100 bound to Low Density Lipoprotein Receptor
- 9BD8 4.8 Å, ApoB 100 beta barrel bound to LDLR beta propeller
- 9BD1 5.4 Å, beta/alpha1 region of ApoB 100
- 9BDT 5.4 Å, Apolipoprotein B 100 bound to LDL receptor and legobody
- 9E9R 9.0 Å, The Structure of ApoB100 from Human Low-Density Lipoprotein
- 9EA7 9.0 Å, The Structure of ApoB100 from Human Low-Density Lipoprotein
- 9EAG 9.0 Å, The Structure of ApoB100 from Human Low-Density Lipoprotein
Browse structure collections
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