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(-) Description

Title :  CRYSTAL STRUCTURE OF 304M3-B FAB IN COMPLEX WITH H3K4ME3 PEPTIDE
 
Authors :  T. Hattori, I. S. Dementieva, S. P. Montano, S. Koide
Date :  27 Feb 15  (Deposition) - 10 Feb 16  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  H,L,P
Biol. Unit 1:  H,L,P  (2x)
Keywords :  Antibody, Fab, Head-To-Head Dimerization, H3K4Me3, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Hattori, D. Lai, I. S. Dementieva, S. P. Montano, K. Kurosawa, Y. Zheng, L. R. Akin, K. M. Swist-Rosowska, A. T. Grzybowski, A. Koide, K. Krajewski, B. D. Strahl, N. L. Kelleher, A. J. Ruthenburg, S. Koide
Antigen Clasping By Two Antigen-Binding Sites Of An Exceptionally Specific Antibody For Histone Methylation.
Proc. Natl. Acad. Sci. Usa V. 113 2092 2016
PubMed-ID: 26862167  |  Reference-DOI: 10.1073/PNAS.1522691113

(-) Compounds

Molecule 1 - FAB HEAVY CHAIN
    ChainsH
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainATCC 55244
    Expression System Taxid562
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - FAB LIGHT CHAIN
    ChainsL
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainATCC 55244
    Expression System Taxid562
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 3 - H3K4ME3 PEPTIDE
    ChainsP
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit HLP
Biological Unit 1 (2x)HLP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1GOL7Ligand/IonGLYCEROL
2M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 18)
No.NameCountTypeFull Name
1GOL14Ligand/IonGLYCEROL
2M3L2Mod. Amino AcidN-TRIMETHYLLYSINE
3SO42Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP H:31 , TYR H:32 , GLN H:53 , PHE H:100 , VAL H:101 , ARG H:102 , TRP H:106 , HOH H:412 , HOH H:465binding site for residue GOL H 301
2AC2SOFTWAREPHE H:104 , TRP H:106 , HOH H:454 , M3L P:4 , THR P:6binding site for residue GOL H 302
3AC3SOFTWAREARG H:30 , ASP H:73 , ASN H:74 , ALA H:75 , HOH H:457binding site for residue GOL H 303
4AC4SOFTWAREPHE H:27 , ARG H:98 , HOH H:401binding site for residue GOL H 304
5AC5SOFTWAREARG H:16 , SER H:17binding site for residue GOL H 305
6AC6SOFTWAREGLN L:36 , ARG L:38 , ILE L:57 , PRO L:58 , PHE L:61 , GLY L:80 , ASP L:81binding site for residue GOL L 301
7AC7SOFTWAREPRO L:58 , GLU L:59 , ARG L:60 , ARG L:76binding site for residue GOL L 302
8AC8SOFTWAREGLY L:67 , ASN L:68 , THR L:69binding site for residue SO4 L 303
9AC9SOFTWARETRP H:33 , ASP H:50 , GLY H:103 , TRP H:106 , GOL H:302 , HOH H:427 , ASP L:29 , TRP L:90 , TYR L:97 , HOH L:404 , THR P:3 , THR P:6 , ALA P:7 , HOH P:102binding site for Ligand residues M3L P 4 through GLN P 5 bound to THR P 3

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1H:22 -H:96
2H:148 -H:204
3L:22 -L:87
4L:135 -L:195

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Phe H:154 -Pro H:155
2Glu H:156 -Pro H:157
3Tyr L:141 -Pro L:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YHZ)

(-) Sequences/Alignments

Asymmetric 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 H from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeeeee....eeeeee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yhz H   1 EVQLVETGGGVVQPGRSLRLSCTASGFTFRDYWMSWVRQAPGKGLEWVADIHQDGQVRYYLDAVKGRFTISRDNAKSSLYLQMNSLGAEDTAVYYCARNFVRGFGWHFDLWGRGTLVTVSSASTKGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS 223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     ||144       154       164       174       184       194       204       214         
                                                                                                                                                                 136|                                                                                  
                                                                                                                                                                  141                                                                                  

Chain L from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.....eeeeee..hhhhh..eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeee....eeee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yhz L   4 LTQPPSVSVAPGQTARITCGGTNIGDISVHWYQQRPGQAPLVVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDDSINAYVFGTGTKVTVLRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 214
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213 

Chain P from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 4yhz P   1 ARTkQTARK   9
                               |     
                               4-M3L 

   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 4YHZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        H31_HUMAN | P684311cs9 1ct6 1guw 1o9s 1q3l 2b2t 2b2u 2b2v 2b2w 2c1j 2c1n 2cv5 2kwj 2kwk 2l75 2lbm 2m0o 2ndf 2ndg 2oq6 2ot7 2ox0 2ri7 2uxn 2v89 2vpg 2x0l 3a1b 3afa 3avr 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3b95 3kmt 3kqi 3lqi 3lqj 3o34 3o35 3o37 3qj6 3rig 3riy 3sou 3sow 3u31 3u3d 3u4s 3u5n 3u5o 3u5p 3uee 3uef 3uig 3uii 3uik 3v43 3w96 3w97 3w98 3w99 3wa9 3waa 3wkj 3x1s 3x1t 3x1u 3x1v 3zg6 3zvy 4a0j 4a0n 4a7j 4bd3 4c1q 4f4u 4f56 4ft2 4ft4 4fwf 4hon 4i51 4l7x 4lk9 4lka 4llb 4lxl 4n4h 4qbq 4qbr 4qbs 4tn7 4u68 4up0 4uy4 4x3k 4y6l 4yhp 4ym5 4ym6 4z0r 4z2m 5av5 5av6 5av8 5av9 5avb 5avc 5b24 5b2i 5b2j 5b31 5c11 5c13 5c3i 5cpi 5cpj 5cpk 5d6y 5dah 5fb0 5fb1 5ffv 5gse 5gsu 5gt0 5gt3 5gtc 5hjb 5hjc 5hjd 5hyn 5iql 5j3v 5j9s 5jhn 5jin 5jiy 5jj0 5jrg 5kjh 5kji 5kkl 5m5g 5svx 5svy 5t0k 5t0m 5t1g 5t1i 5t8r 5tbn 5tdr 5tdw 5v21 5v22 5va6

(-) Related Entries Specified in the PDB File

4yhp 4yhy