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(-) Description

Title :  ALLOSTERIC OPENING OF THE POLYPEPTIDE-BINDING SITE WHEN AN HSP70 BINDS ATP
 
Authors :  R. Qi, E. B. Sarbeng, Q. Liu, K. Q. Le, X. Xu, H. Xu, J. Yang, J. L. Wong, C. Vo W. A. Hendrickson, L. Zhou, Q. Liu
Date :  14 Mar 13  (Deposition) - 29 May 13  (Release) - 07 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dnak, Chaperone, 70Kda Heat Shock Protein (Hsp70), Single-Wavelength Anomalous Diffraction (Sad), Native Structure Determination, Multiple Crystals (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Qi, E. B. Sarbeng, Q. Liu, K. Q. Le, X. Xu, H. Xu, J. Yang, J. L. Wong, C. Vorvis, W. A. Hendrickson, L. Zhou, Q. Liu
Allosteric Opening Of The Polypeptide-Binding Site When An Hsp70 Binds Atp.
Nat. Struct. Mol. Biol. V. 20 900 2013
PubMed-ID: 23708608  |  Reference-DOI: 10.1038/NSMB.2583

(-) Compounds

Molecule 1 - CHAPERONE PROTEIN DNAK
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSMT
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 2-610
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 19)

Asymmetric/Biological Unit (4, 19)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2GOL4Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION
4SO411Ligand/IonSULFATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREATP A:1002 , HOH A:1101 , HOH A:1103 , HOH A:1439 , HOH A:1573BINDING SITE FOR RESIDUE MG A 1001
02AC2SOFTWAREGLY A:10 , THR A:11 , THR A:12 , ASN A:13 , LYS A:70 , GLY A:196 , GLY A:197 , GLY A:198 , ALA A:199 , GLY A:229 , GLU A:267 , LYS A:270 , ILE A:271 , SER A:274 , GLY A:341 , GLY A:342 , GLN A:343 , ARG A:345 , MG A:1001 , HOH A:1101 , HOH A:1103 , HOH A:1105 , HOH A:1108 , HOH A:1115 , HOH A:1119 , HOH A:1173 , HOH A:1181 , HOH A:1247 , HOH A:1439 , HOH A:1573 , HOH B:1196BINDING SITE FOR RESIDUE ATP A 1002
03AC3SOFTWAREARG A:25 , ARG A:34 , GOL A:1008 , HOH A:1163 , HOH A:1329 , ASN B:366BINDING SITE FOR RESIDUE SO4 A 1003
04AC4SOFTWAREARG A:445 , LYS A:446 , HOH A:1189 , HOH A:1511BINDING SITE FOR RESIDUE SO4 A 1004
05AC5SOFTWAREARG A:188 , ARG A:362BINDING SITE FOR RESIDUE SO4 A 1005
06AC6SOFTWARESER A:427 , MET A:428 , GLY A:429 , GLY A:430 , HOH A:1425 , MET B:428 , SO4 B:1006BINDING SITE FOR RESIDUE SO4 A 1006
07AC7SOFTWAREARG A:467 , SER A:545 , LYS A:548 , VAL B:407 , ARG B:447BINDING SITE FOR RESIDUE SO4 A 1007
08AC8SOFTWAREARG A:25 , VAL A:26 , LEU A:27 , GLU A:28 , SO4 A:1003 , ASN B:366BINDING SITE FOR RESIDUE GOL A 1008
09AC9SOFTWAREARG A:84 , ARG A:235 , ARG A:315BINDING SITE FOR RESIDUE GOL A 1009
10BC1SOFTWAREATP B:1002 , HOH B:1101 , HOH B:1102 , HOH B:1347 , HOH B:1432BINDING SITE FOR RESIDUE MG B 1001
11BC2SOFTWAREHOH A:1147 , GLY B:10 , THR B:11 , THR B:12 , ASN B:13 , LYS B:70 , GLY B:196 , GLY B:197 , GLY B:198 , ALA B:199 , GLY B:229 , GLU B:267 , LYS B:270 , SER B:274 , GLY B:341 , GLY B:342 , GLN B:343 , ARG B:345 , MG B:1001 , HOH B:1101 , HOH B:1102 , HOH B:1105 , HOH B:1109 , HOH B:1111 , HOH B:1120 , HOH B:1135 , HOH B:1139 , HOH B:1191 , HOH B:1347 , HOH B:1432BINDING SITE FOR RESIDUE ATP B 1002
12BC3SOFTWAREASN A:366 , ARG B:25 , ARG B:34 , GOL B:1009 , HOH B:1383 , HOH B:1407 , HOH B:1605 , HOH B:1646BINDING SITE FOR RESIDUE SO4 B 1003
13BC4SOFTWARELYS A:268 , ARG B:56 , HOH B:1455BINDING SITE FOR RESIDUE SO4 B 1004
14BC5SOFTWAREARG B:188 , ARG B:362BINDING SITE FOR RESIDUE SO4 B 1005
15BC6SOFTWAREMET A:428 , SO4 A:1006 , SER B:427 , MET B:428 , GLY B:429 , GLY B:430 , HOH B:1633BINDING SITE FOR RESIDUE SO4 B 1006
16BC7SOFTWAREVAL A:407 , ARG A:447 , ARG B:467 , SER B:545 , LYS B:548 , HOH B:1494BINDING SITE FOR RESIDUE SO4 B 1007
17BC8SOFTWAREHOH A:1438 , ARG B:445 , LYS B:446 , ARG B:447 , HOH B:1165BINDING SITE FOR RESIDUE SO4 B 1008
18BC9SOFTWAREASN A:366 , HOH A:1225 , ARG B:25 , VAL B:26 , GLU B:28 , ARG B:34 , TYR B:130 , SO4 B:1003 , HOH B:1167BINDING SITE FOR RESIDUE GOL B 1009
19CC1SOFTWAREASP B:231 , ARG B:235 , ARG B:315 , HOH B:1451 , HOH B:1588BINDING SITE FOR RESIDUE GOL B 1010

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JN4)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile A:418 -Pro A:419
2Ile B:418 -Pro B:419

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JN4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JN4)

(-) Exons   (0, 0)

(no "Exon" information available for 4JN4)

(-) 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:600
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee...eeeeeeee..eeee.........ee.eeee.....eeehhhhhhhhhhhhh.eee.hhhh......hhhhhhhhhhh..eeee.....eeeee..eeehhhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhh......eeeeeeee....eeeeeeeeeee..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeeee..eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeeeehhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh.....eeee......eeeee...eeeeee.......eeeeeeee....eeeeeee....hhhhheeeeeeee............eeeeeee.....eeeeeee.....ee..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jn4 A   1 SGKIIGIDLGTTNSCVAIMDGTTPRVLENAEGDRTTPSIIAYTQDGETLVGQPAKRQAVTNPQNTLFAIKRLIGRRFQDEEVQRDVSIMPFKIIAADNGDAWVEVKGQKMAPPQISAEVLKKMKKTAEDYLGEPVTEAVITVPAYFNDAQRQATKDAGRIAGLEVKRIINEPTAAALAYGLDKGTGNRTIAVYDLGGGAFDISIIEIDEVDGEKTFEVLATNGDTHLGGEDFDSRLINYLVEEFKKDQGIDLRNDPLAMQRLKEAAEKAKIELSSAQQTDVNLPYITADATGPKHMNIKVTRAKLESLVEDLVNRSIEPLKVALQDAGLSVSDIDDVILVGGQTRMPMVQKKVAEFFGKEPRKDVNPDEAVAIGAAVQGGVLTGDVKDVLLLDVTPLSLGIETMGGVMTTLIAKNTTIPTKHSQVFSMGGAVTIHVLQGERKRAADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGLNEDEIQKMVRDAEANAEADRKFEELVQTRNQGDHLLHSTRKQVEEAGDKLPADDKTAIESALTALETALKGEDKAAIEAKMQELAQVSQKLMEIAQQ 604
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430|      444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604
                                                                                                                                                                                                                                                                                                                                                                                                                                                                       430|                                                                                                                                                                         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                        435                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:600
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee...eeeeeeee..eeee.........ee.eeee.....eeehhhhhhhhhhh...eee.hhhh......hhhhhhhhhhh..eeee.....eeeee..eeehhhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhh......eeeeeeee....eeeeeeeeeee..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh....eeeeeeeeee......eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeeeehhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh.....eeee......eeeee...eeeeee.......eeeeeeee....eeeeeee....hhhhheeeeeeee............eeeeeee.....eeeeeee.........eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jn4 B   1 SGKIIGIDLGTTNSCVAIMDGTTPRVLENAEGDRTTPSIIAYTQDGETLVGQPAKRQAVTNPQNTLFAIKRLIGRRFQDEEVQRDVSIMPFKIIAADNGDAWVEVKGQKMAPPQISAEVLKKMKKTAEDYLGEPVTEAVITVPAYFNDAQRQATKDAGRIAGLEVKRIINEPTAAALAYGLDKGTGNRTIAVYDLGGGAFDISIIEIDEVDGEKTFEVLATNGDTHLGGEDFDSRLINYLVEEFKKDQGIDLRNDPLAMQRLKEAAEKAKIELSSAQQTDVNLPYITADATGPKHMNIKVTRAKLESLVEDLVNRSIEPLKVALQDAGLSVSDIDDVILVGGQTRMPMVQKKVAEFFGKEPRKDVNPDEAVAIGAAVQGGVLTGDVKDVLLLDVTPLSLGIETMGGVMTTLIAKNTTIPTKHSQVFSMGGAVTIHVLQGERKRAADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGLNEDEIQKMVRDAEANAEADRKFEELVQTRNQGDHLLHSTRKQVEEAGDKLPADDKTAIESALTALETALKGEDKAAIEAKMQELAQVSQKLMEIAQQ 604
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430|      444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604
                                                                                                                                                                                                                                                                                                                                                                                                                                                                       430|                                                                                                                                                                         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                        435
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 4JN4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JN4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JN4)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DNAK_ECOLI | P0A6Y8: 1bpr 1dg4 1dkg 1dkx 1dky 1dkz 1q5l 2bpr 2kho 3dpo 3dpp 3dpq 3qnj 4b9q 4e81 4ezn 4ezo 4ezp 4ezq 4ezr 4ezs 4ezt 4ezu 4ezv 4ezw 4ezx 4ezy 4ezz 4f00 4f01 4hy9 4hyb 4jne 4jnf 4jwc 4jwd 4jwe 4jwi 4r5g 4r5i 4r5j 4r5k 4r5l

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