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(-) Description

Title :  CRYSTAL STRUCTURE OF RED ABALONE VERL REPEAT 3 AT 2.9 A RESOLUTION
 
Authors :  H. Sadat Al-Hosseini, I. Raj, K. Nishimura, L. Jovine
Date :  01 Mar 16  (Deposition) - 14 Jun 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cell Adhesion, Fertilization, Egg-Sperm Interaction, Gamete Recognition, Vitelline Envelope, Sperm Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Raj, H. Sadat Al Hosseini, E. Dioguardi, K. Nishimura, L. Han, A. Villa, D. De Sanctis, L. Jovine
Structural Basis Of Egg Coat-Sperm Recognition At Fertilization.
Cell V. 169 1315 2017
PubMed-ID: 28622512  |  Reference-DOI: 10.1016/J.CELL.2017.05.033
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MALTOSE-BINDING PERIPLASMIC PROTEIN,VITELLINE ENVELOPE SPERM LYSIN RECEPTOR
    Chains: A, B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK-293S
    Expression System Common: HUMAN
    Expression System Plasmid: PHLSEC
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: MALE, B4034, JW3994, VERL
    Organism Common: CALIFORNIA RED ABALONE
    Organism Scientific: ESCHERICHIA COLI, HALIOTIS RUFESCENS
    Organism Taxid: 83333, 6454
    Other Details: THIS PROTEIN IS A CHIMERA. RESIDUES 3969-4336 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 26-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS A3969T, D4051A, K4052A, E4141A, N4142A, A4184H, K4188H, K4208A, A4281V, I4286V, E4328A, E4331A, D4332A AND R4336N (CORRESPONDING TO A26T, D108A, K109A, E198A, N199A, A241H, K245H, K265A, A338V, I343V, E385A, E388A, D389A AND R393N IN P0AEX9). RESIDUES 4340-4453 ARE FROM RED ABALONE VITELLINE ENVELOPE SPERM LYSIN RECEPTOR AND CORRESPOND TO RESIDUES 340-453 OF SWISS-PROT DATABASE ENTRY Q8WR62.
    Strain: K12
    Synonym: MBP,MMBP,MALTODEXTRIN-BINDING PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1MAL2Ligand/IonMALTOSE
2NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:3981 , ASP A:3983 , LYS A:3984 , TRP A:4031 , ALA A:4032 , ASP A:4034 , ARG A:4035 , GLU A:4080 , GLU A:4122 , PRO A:4123 , TYR A:4124binding site for residue MAL A 4501
2AC2SOFTWAREASN B:3981 , ASP B:3983 , LYS B:3984 , TRP B:4031 , ALA B:4032 , ASP B:4034 , ARG B:4035 , GLU B:4080 , GLU B:4122 , PRO B:4123 , TYR B:4124 , PHE B:4125 , TRP B:4309 , ARG B:4313binding site for residue MAL B 4501
3AC3SOFTWAREASN A:4373 , TRP A:4409binding site for Mono-Saccharide NAG A 4502 bound to ASN A 4373
4AC4SOFTWAREGLN A:4121 , ASP A:4176 , ASN A:4417 , THR A:4419 , VAL A:4420binding site for Mono-Saccharide NAG A 4503 bound to ASN A 4417
5AC5SOFTWAREASN B:4373 , TRP B:4409binding site for Mono-Saccharide NAG B 4502 bound to ASN B 4373
6AC6SOFTWAREARG B:4323 , ASN B:4417 , VAL B:4420binding site for Mono-Saccharide NAG B 4503 bound to ASN B 4417

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:4345 -A:4443
2A:4374 -A:4406
3B:4345 -B:4443
4B:4374 -B:4406

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:4410 -Pro A:4411
2Gly B:4410 -Pro B:4411

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IIC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IIC)

(-) Exons   (0, 0)

(no "Exon" information available for 5IIC)

(-) 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:472
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee....hhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhh......eeeeehhhhhhhhhh........hhhhhhh.hhhhhhhhee..ee..eeeeee..eeeee.........hhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhh..eeeeee..eeeeeeee..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..eeeeeehhhhhhhhhhh...eeee............eeeeeeeee.....hhhhhhhhhhhh..hhhhhhhhhhhh...ee.hhhhhhhhh.hhhhhhhhhhhhhhee.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..eeee........eeeeee......eeeeee..eeeee...eeeeeee..........ee.eeeeee..eeeeeeeeeeeeee......eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5iic A 3969 TKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYAAGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEHAFNHGETAMTINGPWAWSNIDTSAVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELVKDPRVAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAALAAAQTNAAADWDVYCSQDESIPAKFISRLVTALEKTEINCSNGLVPITFGINMMLIQYTRNELSPGMCVFWGPYSVPKNDTVVLYTVTARLKWSEGPPTNLSIQCYMPKS 4448
                                  3978      3988      3998      4008      4018      4028      4038      4048      4058      4068      4078      4088      4098      4108      4118      4128      4138      4148      4158      4168      4178      4188      4198      4208      4218      4228      4238      4248      4258      4268      4278      4288      4298      4308      4318      4328      4338      4348      4358  ||  4372      4382|     4394    ||4406      4416      4426      4436      4446  
                                                                                                                                                                                                                                                                                                                                                                                                                                 4361|            4382|          4399|                                              
                                                                                                                                                                                                                                                                                                                                                                                                                                  4366             4385           4402                                              


Chain B from PDB  Type:PROTEIN  Length:467
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhh....eeeeehhhhhhhhhh........hhhhhhhhhhhhhhhhee..ee..eeeeee..eeeee.........hhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhh.....eee..eee.......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..eeeeeehhhhhhhhhhh...eeee............eeeeeeeee.....hhhhhhhhhhhh..hhhhhhhhhhhh...ee.hhhhhhhhh.hhhhhhhhhhhhhhee....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..eeee........eeeee........eeeeee..eeeeee....eeeeeee..........ee....eee..eeeeeeeeeeeeee...eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5iic B 3974 GKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYAAGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEHAFNHGETAMTINGPWAWSNIDTSAVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELVKDPRVAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAALAAAQTNAAADWDVYCSQDESIPAKFISRLVTSALEKTEINCSNGLVPITQEFGINMMLIQYTRNEDSPGMCVFWGPYSVPKNDTVVLYTVTARLKWSPTNLSIQCYMPKS 4448
                                  3983      3993      4003      4013      4023      4033      4043      4053      4063      4073      4083      4093      4103      4113      4123      4133      4143      4153      4163      4173      4183      4193      4203      4213      4223      4233      4243      4253      4263      4273      4283      4293      4303      4313      4323      4333      4343      4353      4366      4376      4386      4396 ||   4408      4418      4428   || 4441       
                                                                                                                                                                                                                                                                                                                                                                                                                             4362|                            4398|                           4432|            
                                                                                                                                                                                                                                                                                                                                                                                                                              4366                             4401                            4436
   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 5IIC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IIC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IIC)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)

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    Gly A:4410 - Pro A:4411   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        MALE_ECOLI | P0AEX9: 1a7l 1anf 1dmb 1ez9 1ezo 1ezp 1fqa 1fqb 1fqc 1fqd 1hsj 1iud 1jvx 1jvy 1jw4 1jw5 1lax 1lls 1mdp 1mdq 1mg1 1mh3 1mh4 1mpb 1mpc 1mpd 1n3w 1n3x 1nl5 1nmu 1omp 1peb 1r6z 1svx 1t0k 1y4c 1ytv 1ziu 1zjl 1zkb 1zmg 2d21 2h25 2klf 2mv0 2n44 2n45 2nvu 2obg 2ok2 2r6g 2v93 2vgq 2xz3 2zxt 3a3c 3c4m 3csb 3csg 3d4c 3d4g 3dm0 3ef7 3ehs 3eht 3ehu 3f5f 3g7v 3g7w 3h3g 3h4z 3hpi 3hst 3io4 3io6 3ior 3iot 3iou 3iov 3iow 3j9p 3kjt 3l2j 3lbs 3lc8 3mbp 3mp1 3mp6 3mp8 3mq9 3n94 3o3u 3oai 3osq 3osr 3pgf 3puv 3puw 3pux 3puy 3puz 3pv0 3py7 3q25 3q26 3q27 3q28 3q29 3rlf 3rum 3ser 3ses 3set 3seu 3sev 3sew 3sex 3sey 3vfj 3w15 3wai 3woa 4b3n 4bl8 4bl9 4bla 4blb 4bld 4dxb 4dxc 4edq 4egc 4exk 4fe8 4feb 4fec 4fed 4giz 4gli 4ifp 4ikm 4irl 4jbz 4jkm 4keg 4khz 4ki0 4kv3 4kyc 4kyd 4kye 4log 4mbp 4n4x 4ndz 4o2x 4ogm 4pe2 4qsz 4qvh 4r0y 4rg5 4rwf 4rwg 4tsm 4wjv 4wms 4wmt 4wmu 4wmv 4wmw 4wmx 4wrn 4wth 4wvh 4xa2 4xhs 4xr8 4xzs 4xzv 5aq9 5az6 5az7 5az8 5az9 5aza 5b3w 5b3x 5b3y 5b3z 5c7r 5cbn 5cfv 5dfm 5dis 5e24 5edu 5fio 5fsg 5gru 5gs2 5h7n 5h7q 5hz7 5hzv 5hzw 5i04 5i69 5ihj 5ii5 5iqz 5jj4 5jst 5jtq 5jtr 5ldf 5t03 5t05 5t0a 5ttd 5wpz 5wq6
        Q8WR62_HALRU | Q8WR62: 5ii4 5ii5 5iia 5iib 5mr2 5mr3

(-) Related Entries Specified in the PDB File

3d4c
3d4g
3ef7
3nk3
3nk4 RELATED ID: D_1000218160 RELATED DB: PDB RELATED ENTRY UNDER SUBMISSION RELATED ID: D_1000218190 RELATED DB: PDB RELATED ENTRY UNDER SUBMISSION RELATED ID: D_1000218323 RELATED DB: PDB RELATED ENTRY UNDER SUBMISSION