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(-) Description

Title :  CRYO-EM STRUCTURE OF THE FULL-LENGTH HUMAN NPC1 AT 4.4 ANGSTROM
 
Authors :  X. Gong, H. W. Qian, X. H. Zhou, J. P. Wu, Q. Zhou, N. Yan
Date :  01 May 16  (Deposition) - 01 Jun 16  (Release) - 08 Jun 16  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  4.43
Chains :  Asym./Biol. Unit :  A
Keywords :  Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Gong, H. W. Qiang, X. H. Zhou, J. P. Wu, Q. Zhou, N. Yan
The Structure Of Niemann-Pick C1 Protein
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NIEMANN-PICK C1 PROTEIN
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Plasmid: PCAG
    Expression System Strain: HEK 293F
    Expression System Taxid: 9606
    Gene: NPC1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 25)

Asymmetric/Biological Unit (4, 25)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2CLR1Ligand/IonCHOLESTEROL
3MAN1Ligand/IonALPHA-D-MANNOSE
4NAG21Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:65 , CYS A:109 , GLU A:110 , ASN A:222 , NAG A:1302BINDING SITE FOR RESIDUE NAG A 1301
02AC2SOFTWAREGLY A:65 , PHE A:68 , NAG A:1301BINDING SITE FOR RESIDUE NAG A 1302
03AC3SOFTWAREASN A:158 , SER A:244BINDING SITE FOR RESIDUE NAG A 1303
04AC4SOFTWAREASN A:524 , NAG A:1305BINDING SITE FOR RESIDUE NAG A 1304
05AC5SOFTWAREGLN A:88 , NAG A:1304BINDING SITE FOR RESIDUE NAG A 1305
06AC6SOFTWARELYS A:417 , ASP A:551 , ASN A:554 , ASN A:557 , NAG A:1307BINDING SITE FOR RESIDUE NAG A 1306
07AC7SOFTWARENAG A:1306 , BMA A:1308BINDING SITE FOR RESIDUE NAG A 1307
08AC8SOFTWAREASP A:428 , NAG A:1307BINDING SITE FOR RESIDUE BMA A 1308
09AC9SOFTWARETYR A:571 , ASN A:572BINDING SITE FOR RESIDUE NAG A 1309
10BC1SOFTWAREASN A:598 , NAG A:1311BINDING SITE FOR RESIDUE NAG A 1310
11BC2SOFTWARENAG A:1310BINDING SITE FOR RESIDUE NAG A 1311
12BC3SOFTWARETYR A:475 , ASN A:476 , ASN A:478 , NAG A:1313BINDING SITE FOR RESIDUE NAG A 1312
13BC4SOFTWARENAG A:1312 , BMA A:1314 , MAN A:1315BINDING SITE FOR RESIDUE NAG A 1313
14BC5SOFTWARENAG A:1313 , MAN A:1315BINDING SITE FOR RESIDUE BMA A 1314
15BC6SOFTWARENAG A:1313 , BMA A:1314BINDING SITE FOR RESIDUE MAN A 1315
16BC7SOFTWAREASN A:122 , MET A:217BINDING SITE FOR RESIDUE NAG A 1316
17BC8SOFTWAREASN A:70BINDING SITE FOR RESIDUE NAG A 1317
18BC9SOFTWARENAG A:1319BINDING SITE FOR RESIDUE NAG A 1318
19CC1SOFTWAREALA A:183 , ASN A:185 , THR A:187 , ASN A:188 , NAG A:1318BINDING SITE FOR RESIDUE NAG A 1319
20CC2SOFTWAREASN A:1064BINDING SITE FOR RESIDUE NAG A 1320
21CC3SOFTWAREASN A:1072BINDING SITE FOR RESIDUE NAG A 1321
22CC4SOFTWAREASN A:135BINDING SITE FOR RESIDUE NAG A 1322
23CC5SOFTWAREASN A:452BINDING SITE FOR RESIDUE NAG A 1323
24CC6SOFTWAREASN A:459BINDING SITE FOR RESIDUE NAG A 1324
25CC7SOFTWAREASN A:41 , GLN A:79 , ASN A:86 , PHE A:108 , LEU A:111 , THR A:112 , LEU A:176 , TYR A:192 , MET A:193 , PRO A:202 , PHE A:203BINDING SITE FOR RESIDUE CLR A 1325

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:25 -A:74
2A:31 -A:42
3A:63 -A:109
4A:75 -A:113
5A:97 -A:238
6A:100 -A:160
7A:177 -A:184
8A:227 -A:243
9A:468 -A:479
10A:516 -A:533

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Gly A:248 -Pro A:249
2Pro A:377 -Val A:378
3Tyr A:423 -Pro A:424
4Ser A:473 -Pro A:474
5Phe A:924 -Asn A:925
6Asp A:948 -Trp A:949
7Glu A:985 -Gly A:986
8Gly A:1034 -Ala A:1035

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JD8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3JD8)

(-) Exons   (0, 0)

(no "Exon" information available for 3JD8)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:1133
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee..eeeeee.....ee.hhhhhhhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhh.eeeeeeeeee......eeeeeeeeeeeehhhhhhhhhhhhh..........hhhhhh.......hhhhhhhhhhhhhhh....eeeeee..................................................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhh...eeeeeeee......ee..........eehhhhhhhhhhhhhhhhhhhhh.eeee..eeeehhhhh..............hhhhhhh.hhhhhhh.ee....eee..hhhhhhhh........................hhhh.ee.....hhhhh.eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh.....eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhh......................................................................................hhhhhhhhh.hhhhhhhhh.........................................hhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3jd8 A   23 QSCVWYGECGIAYGDKRYNCEYSGPPKPLPKDGYDLVQELCPGFFFGNVSLCCDVRQLQTLKDNLQLPLQFLSRCPSCFYNLLNLFCELTCSPRQSQFLNVTATEDYVDPVTNQTKTNVKELQYYVGQSFANAMYNACRDVEAPSSNDKALGLLCGKDADACNATNWIEYMFNKDNGQAPFTITPVFSDFPVHGMEPMNNATKGCDESVDEVTAPCSCQDCSIVCGPKPQPPPPPAPWTILGLDAMYVIMWITYMAFLLVFFGAFFAFEGCLRRLFTRWGSFCVRNPGCVIFFSLVFITACSSGLVFVRVTTNPVDLWSAPSSQARLEKEYFDQHFGPFFRTEQLIIRAPLTDKHIYQPYPSGADVPFGPPLDIQILHQVLDLQIAIENITASYDNETVTLQDICLAPLSPYNTNCTILSVLNYFQNSHSVLDHKKGDDFFVYADYHTHFLYCVRAPASLNDTSLLHDPCLGTFGGPVFPWLVLGGYDDQNYNNATALVITFPVNNYYNDTEKLQRAQAWEKEFINFVKNYKNPNLTISFTAERSIEDELNRESDSDVFTVVISYAIMFLYISLALGHMKSCRRLLVDSKVSLGIAGILIVLSSVACSLGVFSYIGLPLTLIVIEVIPFLVLAVGVDNIFILVQAYQRDERLQGETLDQQLGRVLGEVAPSMFLSSFSETVAFFLGALSVMPAVHTFSLFAGLAVFIDFAEDGTSVQASESCLFRFFKNSYSPLLLKDWMRPIVIAIFVGVLSFSIAVLNKVDIGLDQSLSMPDDSYMVDYFKSISQYLHAGPPVYFVLEEGHDYTSSKGQNMVCGGMGCNNDSLVQQIFNAAQLDNYTRIGFAPSSWIDDYFDWVKPQSSCCRVPEGKQRPQGGDFMRFLPMFLSDNPNPKCGKGGHAAYSSAVNILLGHGTRVGATYFMTYHTVLQTSADFIDALKKARLIASNVTETMGINGSAYRVFPYSVFYVFYEQYLTIIDDTIFNLGVSLGAIFLVTMVLLGCELWSAVIMCATIAMVLVNMFGVMWLWGISLNAVSLVNLVMSCGISVEFCSHITRAFTVSMKGSRVERAEEALAHMGSSVFSGITLTKFGGIVVLAFAKSQIFQIFYFRMYLAMVLLGATHGLIFLPVLLSYI 1251
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282     ||333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954    || 988       998      1008      1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118      1128      1138      1148      1158      1168      1178      1188      1198      1208      1218      1228      1238      1248   
                                                                                                                                                                                                                                                                                                   288|                                                                                                                                                                                                                                                                                                                                                                                                                                                       772|                                                                                                                                                        959|                                                                                                                                                                                                                                                                           
                                                                                                                                                                                                                                                                                                    330                                                                                                                                                                                                                                                                                                                                                                                                                                                        804                                                                                                                                                         984
   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3JD8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3JD8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3JD8)

(-) Gene Ontology  (47, 47)

Asymmetric/Biological Unit(hide GO term definitions)

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  3jd8
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  NPC1_HUMAN | O15118
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 Related Entries

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UniProtKB/Swiss-Prot
        NPC1_HUMAN | O15118: 3gkh 3gki 3gkj 5f18 5f1b 5hns 5i31 5jnx 5kwy

(-) Related Entries Specified in the PDB File

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