3BGF - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   X-RAY CRYSTAL STRUCTURE OF THE SARS CORONAVIRUS SPIKE RECEPTOR BINDING DOMAIN IN COMPLEX WITH F26G19 FAB

Authors :   J. E. Pak, J. M. Rini

Date :   26 Nov 07 (Deposition) - 02 Dec 08 (Release) - 19 May 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Antigen-Antibody Complex, Envelope Protein, Glycoprotein, Host-Virus Interaction, Membrane, Transmembrane, Virion, Virulence, Viral Protein/Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. E. Pak, C. Sharon, M. Satkunarajah, T. C. Auperin, C. M. Cameron, D. J. Kelvin, J. Seetharaman, A. Cochrane, F. A. Plummer, J. D. Berry, J. M. Rini
Structural Insights Into Immune Recognition Of The Severe Acute Respiratory Syndrome Coronavirus S Protein Receptor Binding Domain.
J. Mol. Biol. V. 388 815 2009
PubMed-ID: 19324051 | Reference-DOI: 10.1016/J.JMB.2009.03.042
(for further references see the PDB file header)

Molecule 1 - SPIKE PROTEIN S1
	Chains	:	S, A
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Plasmid	:	PPA-TEV
	Expression System Strain	:	HEK293T
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Gene	:	S
	Organism Common	:	SARS-COV
	Organism Scientific	:	SARS CORONAVIRUS
	Organism Taxid	:	227859
	Strain	:	TOR2

Molecule 2 - F26G19 FAB
	Chains	:	L, C
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	HYBRIDOMA

Molecule 3 - F26G19 FAB
	Chains	:	H, B
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	HYBRIDOMA

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3BGF)

(no "Site" information available for 3BGF)

Asymmetric Unit

No.	Residues
1	A:323	-	A:348
2	A:366	-	A:419
3	A:467	-	A:474
4	B:22	-	B:92
5	B:142	-	B:197
6	C:23	-	C:88
7	C:134	-	C:194
8	H:22	-	H:92
9	H:142	-	H:197
10	L:23	-	L:88
11	L:134	-	L:194
12	S:323	-	S:348
13	S:366	-	S:419
14	S:467	-	S:474

Asymmetric Unit

No.	Residues
1	Pro S:469	-	Pro S:470
2	Pro A:469	-	Pro A:470
3	Ser L:7	-	Pro L:8
4	Tyr L:94	-	Pro L:95
5	Tyr L:140	-	Pro L:141
6	Ile H:97	-	Pro H:98
7	Phe H:148	-	Pro H:149
8	Glu H:150	-	Pro H:151
9	Trp H:190	-	Pro H:191
10	Ser C:7	-	Pro C:8
11	Tyr C:94	-	Pro C:95
12	Tyr C:140	-	Pro C:141
13	Ile B:97	-	Pro B:98
14	Phe B:148	-	Pro B:149
15	Glu B:150	-	Pro B:151
16	Trp B:190	-	Pro B:191

Asymmetric Unit (9, 18)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_SPIKE_CVHSA_014 *	K	344	R	SPIKE_CVHSA	---	---	A/S	K	344	R
2	UniProt	VAR_SPIKE_CVHSA_015 *	F	360	S	SPIKE_CVHSA	---	---	A/S	F	360	S
3	UniProt	VAR_SPIKE_CVHSA_016 *	R	426	G	SPIKE_CVHSA	---	---	A/S	R	426	G
4	UniProt	VAR_SPIKE_CVHSA_017 *	N	437	D	SPIKE_CVHSA	---	---	A/S	N	437	D
5	UniProt	VAR_SPIKE_CVHSA_018 *	L	472	P	SPIKE_CVHSA	---	---	A/S	L	472	P
6	UniProt	VAR_SPIKE_CVHSA_019 *	N	479	K	SPIKE_CVHSA	---	---	A/S	N	479	K
7	UniProt	VAR_SPIKE_CVHSA_020 *	D	480	G	SPIKE_CVHSA	---	---	A/S	D	480	G
8	UniProt	VAR_SPIKE_CVHSA_021 *	T	487	S	SPIKE_CVHSA	---	---	A/S	T	487	S
9	UniProt	VAR_SPIKE_CVHSA_022 *	F	501	Y	SPIKE_CVHSA	---	---	A/S	F	501	Y
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (9, 9)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_SPIKE_CVHSA_014 *	K	344	R	SPIKE_CVHSA	---	---	A	K	344	R
2	UniProt	VAR_SPIKE_CVHSA_015 *	F	360	S	SPIKE_CVHSA	---	---	A	F	360	S
3	UniProt	VAR_SPIKE_CVHSA_016 *	R	426	G	SPIKE_CVHSA	---	---	A	R	426	G
4	UniProt	VAR_SPIKE_CVHSA_017 *	N	437	D	SPIKE_CVHSA	---	---	A	N	437	D
5	UniProt	VAR_SPIKE_CVHSA_018 *	L	472	P	SPIKE_CVHSA	---	---	A	L	472	P
6	UniProt	VAR_SPIKE_CVHSA_019 *	N	479	K	SPIKE_CVHSA	---	---	A	N	479	K
7	UniProt	VAR_SPIKE_CVHSA_020 *	D	480	G	SPIKE_CVHSA	---	---	A	D	480	G
8	UniProt	VAR_SPIKE_CVHSA_021 *	T	487	S	SPIKE_CVHSA	---	---	A	T	487	S
9	UniProt	VAR_SPIKE_CVHSA_022 *	F	501	Y	SPIKE_CVHSA	---	---	A	F	501	Y
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (9, 9)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_SPIKE_CVHSA_014 *	K	344	R	SPIKE_CVHSA	---	---	S	K	344	R
2	UniProt	VAR_SPIKE_CVHSA_015 *	F	360	S	SPIKE_CVHSA	---	---	S	F	360	S
3	UniProt	VAR_SPIKE_CVHSA_016 *	R	426	G	SPIKE_CVHSA	---	---	S	R	426	G
4	UniProt	VAR_SPIKE_CVHSA_017 *	N	437	D	SPIKE_CVHSA	---	---	S	N	437	D
5	UniProt	VAR_SPIKE_CVHSA_018 *	L	472	P	SPIKE_CVHSA	---	---	S	L	472	P
6	UniProt	VAR_SPIKE_CVHSA_019 *	N	479	K	SPIKE_CVHSA	---	---	S	N	479	K
7	UniProt	VAR_SPIKE_CVHSA_020 *	D	480	G	SPIKE_CVHSA	---	---	S	D	480	G
8	UniProt	VAR_SPIKE_CVHSA_021 *	T	487	S	SPIKE_CVHSA	---	---	S	T	487	S
9	UniProt	VAR_SPIKE_CVHSA_022 *	F	501	Y	SPIKE_CVHSA	---	---	S	F	501	Y
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_MOUSE	84-90	2	C:192-198 L:192-198

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_MOUSE	84-90	1	C:192-198 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_MOUSE	84-90	1	- L:192-198

(no "Exon" information available for 3BGF)

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:178
 aligned with SPIKE_CVHSA | P59594 from UniProtKB/Swiss-Prot  Length:1255

    Alignment length:180
                                   332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502
         SPIKE_CVHSA    323 CPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFE  502
               SCOP domains d3bgfa_ A: Spike protein S1                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhh.....hhhhheeeee..........--.....eeeee..............eeeeeeeee.hhhhhh.....hhhhhhh........eeeeeeehhhhhh........eee....................................eee.......hhhh.eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------R---------------S-----------------------------------------------------------------G----------D----------------------------------P------KG------S-------------Y- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3bgf A  323 CPFGEVFNATKFPSVYAWERKKISNCVADYSVL--STFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFE  502
                                   332       342       352  |  | 362       372       382       392       402       412       422       432       442       452       462       472       482       492       502
                                                          355  |                                                                                                                                                
                                                             358

Chain B from PDB  Type:PROTEIN  Length:216
 aligned with Q8CGS2_MOUSE | Q8CGS2 from UniProtKB/TrEMBL  Length:121

    Alignment length:216
                                                                                                                                   106                                                                                                              
                                                                                                                                105  |            121                                                                                               
                                    12        22        32        42        52        62        72        82        92       102  |  | 110       120|        -         -         -         -         -         -         -         -         -      
        Q8CGS2_MOUSE      3 QVQLQQSGTVLARPGTSVKMSCKTSDYTFTNCWIHWIKQRPGQGLEWIGAISLGNSGAWYNQKFKDKAKLTAVTSTNTAYMEVSSLTNEDSAVYYCTREDYYG--QGFPYWGQGTTVTVSS-----------------------------------------------------------------------------------------------    -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3bgfB01 B:1-113 Immunoglobulins                                                                                          3bgfB02 B:114-213 Immunoglobulins                                                             - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee.......eeeeeee......eeeeee......eee.hhhh....eeeehhh.eeeeee...hhhhheeeeeeee.......eeeee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3bgf B    1 EVQLEESGTVLARPGASVKMSCKASGYTFTTYRMHWIKQRPGQGLEWIGAIYPGNSDTTYNQKFKDKAKLTAVTSTSSAYMELSSLTNEDSAVYFCTREGIPQLLRTLDYWGQGTSVTVSSAKTTAPSVYPLAPVCGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEP  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||102       112       122     ||138       148       158       168       178       188       198       208      
                                                                              52A                            82A||               100A|||                         128|                                                                               
                                                                                                              82B|                100B||                          135                                                                               
                                                                                                               82C                 100C|                                                                                                            
                                                                                                                                    100D

Chain C from PDB  Type:PROTEIN  Length:210
 aligned with IGKC_MOUSE | P01837 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:211
                                                                                                                                        1                                                                                                      
                                     -         -         -         -         -         -         -         -         -         -        |2        12        22        32        42        52        62        72        82        92       102 
          IGKC_MOUSE      - ------------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR  103
               SCOP domains d3bgfc1 C:1-107 automated matches                                                                          d3bgfc2 C:108-211 automated matches                                                                      SCOP domains
               CATH domains 3bgfC01 C:1-108 Immunoglobulins                                                                             3bgfC02 C:109-211 Immunoglobulins                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh-..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3bgf C    1 DILMTQSPSSLSASLGERVSLTCRASQEISGYLSWLQEKPDGTIKRLIYAASTLDSGVPKRFSGSRSGSDYSLTISSLESEDFADYYCLQYVSYPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYE-HNSYTCEATHKTSTSPIVKSFNR  211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      |190       200       210 
                                                                                                                                                                                                                    187 |                      
                                                                                                                                                                                                                      189

Chain C from PDB  Type:PROTEIN  Length:210
 aligned with Q7TS98_MOUSE | Q7TS98 from UniProtKB/TrEMBL  Length:236

    Alignment length:211
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232 
        Q7TS98_MOUSE     23 DIKMTQSPSSMYASLGERVTITCKASQDINSYLSWFQQKPGKSPKTLIYRANRLVDGVPSRFSGSGSGQDYSLTISSLEYEDMGIYYCLQYDEFPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR  233
               SCOP domains d3bgfc1 C:1-107 automated matches                                                                          d3bgfc2 C:108-211 automated matches                                                                      SCOP domains
               CATH domains 3bgfC01 C:1-108 Immunoglobulins                                                                             3bgfC02 C:109-211 Immunoglobulins                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh-..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3bgf C    1 DILMTQSPSSLSASLGERVSLTCRASQEISGYLSWLQEKPDGTIKRLIYAASTLDSGVPKRFSGSRSGSDYSLTISSLESEDFADYYCLQYVSYPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYE-HNSYTCEATHKTSTSPIVKSFNR  211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      |190       200       210 
                                                                                                                                                                                                                    187 |                      
                                                                                                                                                                                                                      189

Chain H from PDB  Type:PROTEIN  Length:216
 aligned with Q8CGS2_MOUSE | Q8CGS2 from UniProtKB/TrEMBL  Length:121

    Alignment length:216
                                                                                                                                   106                                                                                                              
                                                                                                                                105  |            121                                                                                               
                                    12        22        32        42        52        62        72        82        92       102  |  | 110       120|        -         -         -         -         -         -         -         -         -      
        Q8CGS2_MOUSE      3 QVQLQQSGTVLARPGTSVKMSCKTSDYTFTNCWIHWIKQRPGQGLEWIGAISLGNSGAWYNQKFKDKAKLTAVTSTNTAYMEVSSLTNEDSAVYYCTREDYYG--QGFPYWGQGTTVTVSS-----------------------------------------------------------------------------------------------    -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3bgfH01 H:1-113 Immunoglobulins                                                                                          3bgfH02 H:114-213 Immunoglobulins                                                             - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee.......eeeeeee.....eeeeeeee....eeee.hhhh....eeeehhh.eeeeee...hhhhheeeeeeee.......eeeee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3bgf H    1 EVQLEESGTVLARPGASVKMSCKASGYTFTTYRMHWIKQRPGQGLEWIGAIYPGNSDTTYNQKFKDKAKLTAVTSTSSAYMELSSLTNEDSAVYFCTREGIPQLLRTLDYWGQGTSVTVSSAKTTAPSVYPLAPVCGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEP  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||102       112       122     ||138       148       158       168       178       188       198       208      
                                                                              52A                            82A||               100A|||                         128|                                                                               
                                                                                                              82B|                100B||                          135                                                                               
                                                                                                               82C                 100C|                                                                                                            
                                                                                                                                    100D

Chain L from PDB  Type:PROTEIN  Length:212
 aligned with IGKC_MOUSE | P01837 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:212
                                                                                                                                        1                                                                                                       
                                     -         -         -         -         -         -         -         -         -         -        |2        12        22        32        42        52        62        72        82        92       102  
          IGKC_MOUSE      - ------------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN  104
               SCOP domains d3bgfl1 L:1-107 automated matches                                                                          d3bgfl2 L:108-212 automated matches                                                                       SCOP domains
               CATH domains 3bgfL01 L:1-108 Immunoglobulins                                                                             3bgfL02 L:109-212 Immunoglobulins                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC -------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3bgf L    1 DILMTQSPSSLSASLGERVSLTCRASQEISGYLSWLQEKPDGTIKRLIYAASTLDSGVPKRFSGSRSGSDYSLTISSLESEDFADYYCLQYVSYPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN  212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain L from PDB  Type:PROTEIN  Length:212
 aligned with Q7TS98_MOUSE | Q7TS98 from UniProtKB/TrEMBL  Length:236

    Alignment length:212
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232  
        Q7TS98_MOUSE     23 DIKMTQSPSSMYASLGERVTITCKASQDINSYLSWFQQKPGKSPKTLIYRANRLVDGVPSRFSGSGSGQDYSLTISSLEYEDMGIYYCLQYDEFPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN  234
               SCOP domains d3bgfl1 L:1-107 automated matches                                                                          d3bgfl2 L:108-212 automated matches                                                                       SCOP domains
               CATH domains 3bgfL01 L:1-108 Immunoglobulins                                                                             3bgfL02 L:109-212 Immunoglobulins                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3bgf L    1 DILMTQSPSSLSASLGERVSLTCRASQEISGYLSWLQEKPDGTIKRLIYAASTLDSGVPKRFSGSRSGSDYSLTISSLESEDFADYYCLQYVSYPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN  212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain S from PDB  Type:PROTEIN  Length:179
 aligned with SPIKE_CVHSA | P59594 from UniProtKB/Swiss-Prot  Length:1255

    Alignment length:179
                                   332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492         
         SPIKE_CVHSA    323 CPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSF  501
               SCOP domains d3bgfs_ S: Spike protein S1                                                                                                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhheeeee......hhhhhh.....eeeee...hhhhh......eeeeeeeee.hhhhhh.....hhhhhhh........eeeeeeehhhhhh........eee....................................eee.......hhhh.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------R---------------S-----------------------------------------------------------------G----------D----------------------------------P------KG------S-------------Y SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3bgf S  323 CPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSF  501
                                   332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492

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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Sars-cov (Sars coronavirus) (1)

1a	3bgfL02	L:109-212
1b	3bgfC02	C:109-211
1c	3bgfC01	C:1-108
1d	3bgfL01	L:1-108
1e	3bgfB02	B:114-213
1f	3bgfH02	H:114-213
1g	3bgfB01	B:1-113
1h	3bgfH01	H:1-113

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

Asymmetric Unit(hide GO term definitions)

Chain A,S (SPIKE_CVHSA | P59594)

molecular function
	GO:0046789	host cell surface receptor binding	Interacting selectively and non-covalently with a receptor on the host cell surface.
biological process
	GO:0039654	fusion of virus membrane with host endosome membrane	Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
	GO:0061025	membrane fusion	The membrane organization process that joins two lipid bilayers to form a single membrane.
	GO:0039663	membrane fusion involved in viral entry into host cell	Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	GO:0046813	receptor-mediated virion attachment to host cell	The process by which a virion attaches to a host cell by binding to a receptor on the host cell surface.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
	GO:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
	GO:0044173	host cell endoplasmic reticulum-Golgi intermediate compartment membrane	The lipid bilayer surrounding any of the compartments of the host cell ER-Golgi intermediate compartment system.
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019031	viral envelope	The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.
	GO:0055036	virion membrane	The lipid bilayer surrounding a virion.

Chain B,H (Q8CGS2_MOUSE | Q8CGS2)

Chain C,L (IGKC_MOUSE | P01837)

molecular function
	GO:0003823	antigen binding	Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
	GO:0034987	immunoglobulin receptor binding	Interacting selectively and non-covalently with one or more specific sites on an immunoglobulin receptor molecule.
biological process
	GO:0030183	B cell differentiation	The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
	GO:0050853	B cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
	GO:0006958	complement activation, classical pathway	Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0006911	phagocytosis, engulfment	The internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis, including the membrane and cytoskeletal processes required, which involves one of three mechanisms: zippering of pseudopods around a target via repeated receptor-ligand interactions, sinking of the target directly into plasma membrane of the phagocytosing cell, or induced uptake via an enhanced membrane ruffling of the phagocytosing cell similar to macropinocytosis.
	GO:0006910	phagocytosis, recognition	The initial step in phagocytosis involving adhesion to bacteria, immune complexes and other particulate matter, or an apoptotic cell and based on recognition of factors such as bacterial cell wall components, opsonins like complement and antibody or protein receptors and lipids like phosphatidyl serine, and leading to intracellular signaling in the phagocytosing cell.
	GO:0050871	positive regulation of B cell activation	Any process that activates or increases the frequency, rate or extent of B cell activation.
cellular component
	GO:0072562	blood microparticle	A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	GO:0042571	immunoglobulin complex, circulating	An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain C,L (Q7TS98_MOUSE | Q7TS98)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3bgf)

	Sites
(no "Sites" information available for 3bgf)

	Cis Peptide Bonds
		Glu B:150 - Pro B:151	[ RasMol ]
		Glu H:150 - Pro H:151	[ RasMol ]
		Ile B:97 - Pro B:98	[ RasMol ]
		Ile H:97 - Pro H:98	[ RasMol ]
		Phe B:148 - Pro B:149	[ RasMol ]
		Phe H:148 - Pro H:149	[ RasMol ]
		Pro A:469 - Pro A:470	[ RasMol ]
		Pro S:469 - Pro S:470	[ RasMol ]
		Ser C:7 - Pro C:8	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Trp B:190 - Pro B:191	[ RasMol ]
		Trp H:190 - Pro H:191	[ RasMol ]
		Tyr C:140 - Pro C:141	[ RasMol ]
		Tyr C:94 - Pro C:95	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]
		Tyr L:94 - Pro L:95	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
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	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

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	3bgf
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	IGKC_MOUSE \| P01837
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	Q7TS98_MOUSE \| Q7TS98
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	Q8CGS2_MOUSE \| Q8CGS2
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		Protein-protein Interaction	:	DIP
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	SPIKE_CVHSA \| P59594
		Comparative Protein Structure Models	:	ModBase
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	Q7TS98_MOUSE \| Q7TS98
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	Q8CGS2_MOUSE \| Q8CGS2
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	SPIKE_CVHSA \| P59594
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2ajf	S RECEPTOR BINDING DOMAIN IN COMPLEX WITH RECEPTOR
2dd8	S RECEPTOR BINDING DOMAIN IN COMPLEX WITH NEUTRALIZING ANTIBODY
2ghv	S RECEPTOR BINDING DOMAIN
2ghw	S RECEPTOR BINDING DOMAIN IN COMPLEX WITH NEUTRALIZING ANTIBODY

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (14, 14)

Cis Peptide Bonds (16, 16)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (9, 18)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 6)

CATH Domains (1, 8)

Pfam Domains (0, 0)

Gene Ontology (31, 43)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File