4XAK - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF POTENT NEUTRALIZING ANTIBODY M336 IN COMPLEX WITH MERS CO-V RBD

Authors :   T. Zhou, D. S. Dimtrov, T. Ying

Date :   15 Dec 14 (Deposition) - 26 Aug 15 (Release) - 23 Sep 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

Chains :   Asym. Unit : A,B,D,E,H,L
Biol. Unit 1: A,H,L  (1x)
Biol. Unit 2: B,D,E  (1x)

Keywords :   Mers-Cov Rbd, Antibody M336, Neutralization, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Ying, P. Prabakaran, L. Du, W. Shi, Y. Feng, Y. Wang, L. Wang, W. Li, S. Jiang, D. S. Dimitrov, T. Zhou
Junctional And Allele-Specific Residues Are Critical For Mers-Cov Neutralization By An Exceptionally Potent Germline-Like Antibody.
Nat Commun V. 6 8223 2015
PubMed-ID: 26370782 | Reference-DOI: 10.1038/NCOMMS9223

Molecule 1 - SPIKE GLYCOPROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	GNTI-/-
	Expression System Common	:	HUMAN
	Expression System Plasmid	:	PVRC8400
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Fragment	:	RECEPTOR-BINDING DOMAIN (UNP RESIDUES 367-601)
	Gene	:	S, 3
	Organism Common	:	HCOV-EMC
	Organism Scientific	:	HUMAN CORONAVIRUS EMC
	Organism Taxid	:	1263720
	Other Details	:	MERS-COV RBD WITH HRV3C CLEAVAGE SITE AND HIS 6X TAG AT THE C-TERMINAL.
	Strain	:	ISOLATE UNITED KINGDOM/H123990006/2012
	Synonym	:	S GLYCOPROTEIN,E2,PEPLOMER PROTEIN

Molecule 2 - HEAVY CHAIN OF NEUTRALIZING ANTIBODY M336
	Chains	:	H, D
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK 293F
	Expression System Common	:	HUMAN
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 3 - LIGHT CHAIN OF NEUTRALIZING ANTIBODY M336
	Chains	:	L, E
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK 293F
	Expression System Common	:	HUMAN
	Expression System Plasmid	:	PLASMID
	Expression System Taxid	:	9606
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	D	E	H	L
Biological Unit 1 (1x)	:	A				H	L
Biological Unit 2 (1x)	:		B	D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE H:166 , PRO H:167 , SER H:177 , LEU H:178 , SER H:179 , GLN L:160 , SER L:162 , SER L:176 , SER L:177 , THR L:178 , HOH L:663	binding site for residue GOL L 500
2	AC2	SOFTWARE	GLN L:37 , LYS L:45 , PRO L:59 , PHE L:62 , GLU L:81 , ASP L:82	binding site for residue GOL L 501
3	AC3	SOFTWARE	ASN A:410 , THR A:412 , LYS A:413 , LYS A:587 , LEU A:588 , GLU A:589 , LYS E:149	binding site for Mono-Saccharide NAG A 701 bound to ASN A 410
4	AC4	SOFTWARE	ASN A:487 , LYS E:145	binding site for Mono-Saccharide NAG A 702 bound to ASN A 487
5	AC5	SOFTWARE	ASN B:410 , LYS B:413 , SER B:416 , LYS B:587 , GLU B:589 , LYS H:210	binding site for Mono-Saccharide NAG B 701 bound to ASN B 410
6	AC6	SOFTWARE	ASN B:487 , LYS L:188	binding site for Mono-Saccharide NAG B 702 bound to ASN B 487

Asymmetric Unit

No.	Residues
1	A:383	-	A:407
2	A:425	-	A:478
3	A:437	-	A:585
4	A:503	-	A:526
5	B:383	-	B:407
6	B:425	-	B:478
7	B:437	-	B:585
8	B:503	-	B:526
9	D:22	-	D:92
10	D:98	-	D:100C
11	D:140	-	D:196
12	E:23	-	E:88
13	E:134	-	E:194
14	H:22	-	H:92
15	H:98	-	H:100C
16	H:140	-	H:196
17	L:23	-	L:88
18	L:134	-	L:194

Asymmetric Unit

No.	Residues
1	Phe H:146	-	Pro H:147
2	Glu H:148	-	Pro H:149
3	Ser L:7	-	Pro L:8
4	Tyr L:94	-	Pro L:95
5	Tyr L:140	-	Pro L:141
6	Phe D:146	-	Pro D:147
7	Glu D:148	-	Pro D:149
8	Ser E:7	-	Pro E:8
9	Tyr E:94	-	Pro E:95
10	Tyr E:140	-	Pro E:141

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

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

(no "Exon" information available for 4XAK)

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 A from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh....hhhhheeeee...eehhhhhhhh.eeeeeeee.............eeeeeeee.hhhhhhhhh....hhhhhhh........eeeeeee.............eeeeeeeeee......eee........hhhhhh.........eeeeee.hhhhh..eeeeeeeee......eeeeeeeee........ee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xak A  381 VECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSLFSVNDFTCSQISPAAIASNCYSSLILDYFSYPLSMKSDLSVSSAGPISQFNYKQSFSNPTCLILATVPHNLTTITKPLKYSYINKCSRFLSDDRTEVPQLVNANQYSPCVSIVPSTVWEDGDYYRKQLSPLEGGGWLVASGSTVAMTEQLQMGFGITVQYGTDTNSVCPKLEFA  591
                                   390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590

Chain B from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh....hhhhheeeee...eehhhhhhhh.eeeeeeee..hhhhhh.....eeeeeeee.hhhhh........hhhhhhh........eeeeeee.............eeeeeeeeee......eee........hhhhhh.........eeeeee.hhhhh..eeeeeeeee......eeeeeeeee........ee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xak B  381 VECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSLFSVNDFTCSQISPAAIASNCYSSLILDYFSYPLSMKSDLSVSSAGPISQFNYKQSFSNPTCLILATVPHNLTTITKPLKYSYINKCSRFLSDDRTEVPQLVNANQYSPCVSIVPSTVWEDGDYYRKQLSPLEGGGWLVASGSTVAMTEQLQMGFGITVQYGTDTNSVCPKLEFA  591
                                   390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590

Chain D from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeeeee.......eeeeee...eeeee........eeeee...eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeehhhhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xak D    1 QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAPGQGLEWMGGIIPIFGTASYAQKFQGRVTITADKSTSTAYMELSSLRSEDTAVYYCARVGYCSSTSCNRGAFDIWGQGTMVTVSSASTKGPSVFPLAPTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||     108       118       136       146       156       166       176       186       196       206        
                                                                              52A                            82A||               100A|||||||                       126|                                                                               
                                                                                                              82B|                100B||||||                        135                                                                               
                                                                                                               82C                 100C|||||                                                                                                          
                                                                                                                                    100D||||                                                                                                          
                                                                                                                                     100E|||                                                                                                          
                                                                                                                                      100F||                                                                                                          
                                                                                                                                       100G|                                                                                                          
                                                                                                                                        100H

Chain E from PDB  Type:PROTEIN  Length:207
                                                                                                                                                                                                                                                
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeee....eeeeee.........eeeeee...........eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeee.....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xak E    1 DIQLTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQLNSYPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150|      164       174       184       194       204       
                                                                                                                                                                               150|                                                        
                                                                                                                                                                                155

Chain H from PDB  Type:PROTEIN  Length:227
                                                                                                                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeeeee.......eeeeee...eeeee........eeeee..hhhhh...eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhh..eeeeeeehhhheeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xak H    1 QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAPGQGLEWMGGIIPIFGTASYAQKFQGRVTITADKSTSTAYMELSSLRSEDTAVYYCARVGYCSSTSCNRGAFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS  215
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||     108       118       128       138       148       158       168       178       188       198       208       
                                                                              52A                            82A||               100A|||||||                                                                                                                   
                                                                                                              82B|                100B||||||                                                                                                                   
                                                                                                               82C                 100C|||||                                                                                                                   
                                                                                                                                    100D||||                                                                                                                   
                                                                                                                                     100E|||                                                                                                                   
                                                                                                                                      100F||                                                                                                                   
                                                                                                                                       100G|                                                                                                                   
                                                                                                                                        100H

Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhh.eeeeee...........eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xak L    1 DIQLTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQLNSYPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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 '\|'

(no "SCOP Domain" information available for 4XAK)

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Glu D:148 - Pro D:149	[ RasMol ]
		Glu H:148 - Pro H:149	[ RasMol ]
		Phe D:146 - Pro D:147	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Ser E:7 - Pro E:8	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Tyr E:140 - Pro E:141	[ RasMol ]
		Tyr E:94 - Pro E:95	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]
		Tyr L:94 - Pro L:95	[ RasMol ]

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	4xak
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	SPIKE_CVEMC \| K9N5Q8	:	4l72 4zpt 4zpv 4zpw

(no "Related Entries Specified in the PDB File" available for 4XAK)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (18, 18)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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