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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

9NVV

Cryo-EM structure of V2 apex germline-targeting HIV Env trimer Q23-APEX-GT2

Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A, C, E
(b, d, f)		HIV envelope gp120polymer76385350.13UniProt (O55774)Human immunodeficiency virus 1Env polyprotein
2B, D, F
(c, e, g)		HIV envelope gp41 ectodomainpolymer15317205.73UniProt (O55774)Human immunodeficiency virus 1Env polyprotein
3AA, BA, CA, DA, EA...
(U, V, W, X, Y...)		2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranosebranched424.428In PDB
GlyTouCan (G42666HT)
4GA, H, HA, MA, N...
(a, B, h, m, H...)		beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranosebranched586.57In PDB
GlyTouCan (G15407YE)
5I
(C)		alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranosebranched748.71In PDB
GlyTouCan (G81315DD)
6U
(O)		alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranosebranched910.81In PDB
GlyTouCan (G22768VO)
7AB, BB, CB, DB, EB...
(c, d, e, f, b...)		2-acetamido-2-deoxy-beta-D-glucopyranosenon-polymer221.232Chemie (NAG)
Sequence modifications
b, d, f: 31 - 618 (UniProt: O55774)
PDBExternal DatabaseDetails
Ala 31Val 30conflict
Glu 49Asp 48conflict
Arg 132Thr 131conflict
Glu 153Gly 144conflict
Thr 158Ser 149conflict
Cys 201Ile 193conflict
Ala 219Thr 211conflict
Tyr 302Asn 294conflict
Met 320Thr 310conflict
Ser 334Thr 325conflict
Cys 433Ala 423conflict
Cys 501Ala 491conflict
Gly 508Arg 498conflict
Gly 509Glu 499conflict
Gly 510Lys 500conflict
Gly 511Arg 501conflict
Ser 512Ala 502conflict
Gly 513Val 503conflict
Gly 515Ile 505conflict
Ser 517Ala 507conflict
Phe 518-insertion
Glu 519-insertion
Pro 520-insertion
Ile 521Val 508conflict
Pro 522Phe 509conflict
Ile 523Leu 510conflict
His 524Gly 511conflict
Tyr 525Phe 512conflict
Cys 526Leu 513conflict
Ala 527Gly 514conflict
Pro 528Ala 515conflict
Phe 531-insertion
Ala 532-insertion
Ile 533-insertion
Leu 534-insertion
Lys 535-insertion
Cys 536-insertion
Lys 537-insertion
Asp 538-insertion
Glu 539-insertion
Gly 540-insertion
Phe 541-insertion
Asn 542-insertion
Gly 543-insertion
Thr 544-insertion
Gly 545-insertion
Leu 546-insertion
Cys 547-insertion
Lys 548-insertion
Asn 549-insertion
Val 550-insertion
Val 553Met 520conflict
Gln 554Gly 521conflict
Cys 555Ala 522conflict
His 557-insertion
Gly 558Ser 524conflict
Lys 560Thr 526conflict
Pro 561Leu 527conflict
Val 562Thr 528conflict
Ser 564Gln 530conflict
Thr 565Ala 531conflict
Gln 566Arg 532conflict
Leu 567Gln 533conflict
Asn 570Ser 536conflict
Ser 572Ile 538conflict
Leu 573Val 539conflict
Ala 574Gln 540conflict
Glu 575Gln 541conflict
Lys 576Gln 542conflict
Ile 578Asn 544conflict
Thr 579Leu 545conflict
Ile 580Leu 546conflict
Ser 582Ala 548conflict
Glu 583Ile 549conflict
Asn 584Glu 550conflict
Ile 585Ala 551conflict
Thr 586Gln 552conflict
Asn 587Gln 553conflict
Asn 588His 554conflict
Ala 589Leu 555conflict
Lys 590Leu 556conflict
Ile 591Lys 557conflict
Ile 592Leu 558conflict
Ile 593Thr 559conflict
Gln 595Trp 561conflict
Leu 596Gly 562conflict
Val 597Ile 563conflict
Gln 598Lys 564conflict
Pro 599Gln 565conflict
Val 600Leu 566conflict
Thr 601Gln 567conflict
Ile 602Ala 568conflict
Lys 603Arg 569conflict
Cys 604Val 570conflict
Ile 605Leu 571conflict
Arg 606Ala 572conflict
Pro 607Val 573conflict
Asn 608Glu 574conflict
Asn 609Arg 575conflict
Thr 611Leu 577conflict
Lys 613Asp 579conflict
Ser 614Gln 580conflict
Ile 615Gln 581conflict
Arg 616Leu 582conflict
Ile 617Leu 583conflict
Pro 619-expression tag
Gly 620-expression tag
Gln 621-expression tag
Ala 622-expression tag
Phe 623-expression tag
Tyr 624-expression tag
Ala 625-expression tag
Met 626-expression tag
Gly 627-expression tag
Asp 628-expression tag
Ile 629-expression tag
Ile 630-expression tag
Gly 631-expression tag
Asp 632-expression tag
Ile 633-expression tag
Arg 634-expression tag
Gln 635-expression tag
Ala 636-expression tag
His 637-expression tag
Cys 638-expression tag
Asn 639-expression tag
Val 640-expression tag
Ser 641-expression tag
Arg 642-expression tag
Ser 643-expression tag
Arg 644-expression tag
Trp 645-expression tag
Asn 646-expression tag
Lys 647-expression tag
Thr 648-expression tag
Leu 649-expression tag
Gln 650-expression tag
Glu 651-expression tag
Val 652-expression tag
Ala 653-expression tag
Glu 654-expression tag
Lys 655-expression tag
Leu 656-expression tag
Arg 657-expression tag
Thr 658-expression tag
Tyr 659-expression tag
Phe 660-expression tag
Gly 661-expression tag
Asn 662-expression tag
Lys 663-expression tag
Thr 664-expression tag
Ile 665-expression tag
Ile 666-expression tag
Phe 667-expression tag
Ala 668-expression tag
Asn 669-expression tag
Ser 670-expression tag
Ser 671-expression tag
Gly 672-expression tag
Gly 673-expression tag
Asp 674-expression tag
Leu 675-expression tag
Glu 676-expression tag
Ile 677-expression tag
Thr 678-expression tag
Thr 679-expression tag
His 680-expression tag
Ser 681-expression tag
Phe 682-expression tag
Asn 683-expression tag
Cys 684-expression tag
Gly 685-expression tag
Gly 686-expression tag
Glu 687-expression tag
Phe 688-expression tag
Phe 689-expression tag
Tyr 690-expression tag
Cys 691-expression tag
Asn 692-expression tag
Thr 693-expression tag
Ser 694-expression tag
Gly 695-expression tag
Leu 696-expression tag
Phe 697-expression tag
Asn 698-expression tag
Ser 699-expression tag
Thr 700-expression tag
Trp 701-expression tag
Tyr 702-expression tag
Val 703-expression tag
Asn 704-expression tag
Ser 705-expression tag
Thr 706-expression tag
Trp 707-expression tag
Asn 708-expression tag
Ser 709-expression tag
Asn 710-expression tag
Asp 711-expression tag
Thr 712-expression tag
Ile 713-expression tag
Thr 714-expression tag
Leu 715-expression tag
Pro 716-expression tag
Cys 717-expression tag
Arg 718-expression tag
Ile 719-expression tag
Lys 720-expression tag
Gln 721-expression tag
Ile 722-expression tag
Ile 723-expression tag
Asn 724-expression tag
Met 725-expression tag
Trp 726-expression tag
Gln 727-expression tag
Arg 728-expression tag
Ala 729-expression tag
Gly 730-expression tag
Gln 731-expression tag
Cys 732-expression tag
Met 733-expression tag
Tyr 734-expression tag
Ala 735-expression tag
Pro 736-expression tag
Pro 737-expression tag
Ile 738-expression tag
Pro 739-expression tag
Gly 740-expression tag
Val 741-expression tag
Ile 742-expression tag
Lys 743-expression tag
Cys 744-expression tag
Glu 745-expression tag
Ser 746-expression tag
Asn 747-expression tag
Ile 748-expression tag
Thr 749-expression tag
Gly 750-expression tag
Leu 751-expression tag
Leu 752-expression tag
Leu 753-expression tag
Thr 754-expression tag
Arg 755-expression tag
Asp 756-expression tag
Gly 757-expression tag
Gly 758-expression tag
Lys 759-expression tag
Asp 760-expression tag
Asn 761-expression tag
Asn 762-expression tag
Val 763-expression tag
Asn 764-expression tag
Glu 765-expression tag
Thr 766-expression tag
Phe 767-expression tag
Arg 768-expression tag
Pro 769-expression tag
Gly 770-expression tag
Gly 771-expression tag
Gly 772-expression tag
Asp 773-expression tag
Met 774-expression tag
Arg 775-expression tag
Asp 776-expression tag
Asn 777-expression tag
Trp 778-expression tag
Arg 779-expression tag
Ser 780-expression tag
Glu 781-expression tag
Leu 782-expression tag
Tyr 783-expression tag
Lys 784-expression tag
Tyr 785-expression tag
Lys 786-expression tag
Val 787-expression tag
Val 788-expression tag
Glu 789-expression tag
Ile 790-expression tag
Glu 791-expression tag
Pro 792-expression tag
Leu 793-expression tag
Gly 794-expression tag
Val 795-expression tag
Ala 796-expression tag
Pro 797-expression tag
Thr 798-expression tag
Arg 799-expression tag
Cys 800-expression tag
Lys 801-expression tag
Arg 802-expression tag
c, e, g: 512 - 664 (UniProt: O55774)
PDBExternal DatabaseDetails
Arg 519Phe 509conflict
Arg 520Leu 510conflict
Ala 533Thr 523conflict
Pro 551Gln 541conflict
Pro 559Ile 549conflict
Gly 569Thr 559conflict
Cys 605Thr 595conflict
Gly 636Asn 626conflict
Ala 662Glu 652conflict
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains6
Total formula weight307667.2
BranchedNumber of molecules37
Total formula weight17648.5
Non-Polymers*Number of molecules32
Total formula weight7078.7
All*Total formula weight332394.3
*Water molecules are not included.

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PDB entries from 2026-04-08

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