Table S1. Neutralization IC 50 and IC 80 Titers (µg/ml) of the Antibody VRC08 against 195 HIV-1 Envpesudoviruses,
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1 Table S. Neutralization IC 50 and IC 80 Titers (µg/ml) of the Antibody 8 against 95 HIV- Envpesudoviruses, Related to Figure Virus Clade IC 50 IC 80 Virus Clade IC 50 IC 80 Virus Clade IC 50 IC v5.c36 A T AG 22.5 > C v4.c3 A T257-3 AG C v5.c A T AG C v2.c20 A T AG >50 > V4.C0 C v.c A T280-5 AG V5.C3 C v3.c A >50 >50 T33-7 AG V.C24 C F_F6_20 A B V4.C C >50 >50 BB20.B42 A B V.C6 C >50 >50 BB539.2B3 A B V3.C0 C BI369.9A A B V2.C33 C BS208.B A B V5.C4 C KER A _0dG5 B V.C35 C KER208. A B ZM65.02 C KNH209.8 A AC0.29 B BR025.9 C MB20.A A ADA B CAP20.E8 C >50 >50 MB539.2B7 A BaL.0 B CAP244.D3 C MI369.A5 A BaL.26 B CAP45.G3 C MS208.A A BG68.0 B CNE30 C Q23.7 A BL0 B >50 >50 CNE3 C Q259.7 A BR07 B CNE53 C Q769.d22 A BX08.6 B CNE58 C Q842.d2 A CAAN.A2 B Du23.06 C QH209.4M.A2 A CNE0 B Du5.02 C RW020.2 A CNE2 B Du56.2 C UG037.8 A CNE4 B Du72.7 C >50 > V.C24 AC CNE4 B Du422.0 C 6.8 > V.C4 AC CNE57 B MW C v4.c AC >50 >50 HO86.8 B >50 >50 SO8.8 C V4.C AC >50 >50 HT593. B TV.29 C >50 > V3.C3 ACD HXB2 B TZA25.7 C >50 > V.C0 ACD JR-CSF B TZBD.02 C V.C2 AD.84 >50 JR-FL B ZA02.29 C Q68.a2 AD MN.3 B ZM06.9 C Q46.e2 AD PVO.04 B ZM09.4 C c AE >50 >50 QH055.0 B ZM35.0a C BJOX AE QH B ZM76.66 C >50 BJOX AE REJO.67 B ZM97.7 C BJOX AE RHPA.7 B ZM24.5 C BJOX AE SC422.8 B ZM25.8 C C080.c3 AE SF62 B ZM249. C C20.c AE SS96.0 B ZM53.2 C C3347.c AE THRO.8 B ZM55.28a C C48.09 AE TRJO.58 B V4.C3 CD >50 >50 CM244.ec AE TRO. B V2.C6 CD CNE3 AE WITO.33 B v2.c59 CD >50 >50 CNE5 AE Yu2 B E6. D CNE55 AE CH038.2 BC c D 7.7 >50 CNE56 AE CH070. BC >50 > D CNE59 AE CH7.4 BC v5.c45 D CNE8 AE CH8.2 BC vrc5 D >50 >50 M0238 AE CNE5 BC v4.c34 D R66.c AE CNE9 BC A03349M.vrc4a D R284.c4 AE CNE20 BC A0742M.vrc2 D R3265.c6 AE CNE2 BC NKU3006.ec D TH023.6 AE CNE40 BC UG024.2 D TH966.8 AE CNE7 BC P0402.c2. G TH976.7 AE C P98.C5.3 G AG C X93.c G AG >50 > C X254.c3 G AG C X632.S2.B0 G 2.88 > AG _V.C6 C >50 >50 X2088.c9 G >50 > AG C AG V2.C4 C DJ263.8 AG C T250-4 AG >50 > C T25-8 AG C T253- AG C
2 Table S2. Clinical and Sequencing Parameters of Donor 45 over 5 Years of HIV- Infection, Related to Figure 2 A Blood drawn date 3/20/995 7/30/200 4/6/2002 7/4/2006 /9/2007 7/2/2007 /7/2008 8/9/2008 6/2/2009 2/3/2009 CD4 count (cells/μl) Plasma viral load (copies/ml) ,000 9,858 9,607 9,29 7,796 2,709 6,920 8,588 5,53 5,58 B 3/995 7/200 4/2002 7/2006 /2007 7/2007 /2008 8/2008 6/2009 2/2009 TOTAL NGS heading O A B C D E F G H I raw heavy 932, , ,4 529,389 39, ,09 220, , , ,209 4,25,004 total heavy with length and V unique* heavy with length and V total crossdonor positives (XD+) 66, , , ,52 39,67 376,939 24,95 475, , ,54 3,936,838 07,736 86,36,66 38,005 93,590 04,09 67,434 08,459 79,47 44,76 84,290 56,855 7,494 6,654 43,652 7,322 7,555 2,43,946 27,797 49, ,253 unique* XD+ 5, ,20,847 2,75 4,537 5,03,800 4,534,83 32,455 total in accepted groups ( AG ) AG with J, in frame, and ORF ( ORF ) 6,875 4,645 8,085 26,545 2,757 7,744 8,778 9,204 6,547 33,654 24,834 4,842 3,005 2,93 7,94,645 3,53 4,297 4,898 8,59 23,040 73,524 ORF unique* ,886 final curated ,04 raw light 89, , , , , ,46 463, , ,276 36,62 4,46,33 total light with length and V unique* light with length and V total 5aa CDR L3 unique* 5 AA CDR L3 total in accepted groups ( AG ) AG with J, in frame, and ORF ( ORF ) 89,65 377,99 455, , , ,44 463,862 64, ,433 36,34 4,4,76 78,402 52,043 95,404 23,380 48,2 64,796 70, ,903 55,439 6, ,088 6, ,329 8,279,3 8,853 4,947 8,323 5,55 6,475 54,398 2,45 275, , , ,322 7, ,994 3,072 3,36 3,245 4,892 28, , ,903 2,335,797 2,39 3,786 9,987 ORF unique* final curated * Uniqueness was defined by clustering at 97.25% identity to account for sequencing error. The pipeline used for this work only takes account of uniqueness in the penultimate filtering step, for open-reading frames among the accepted groups. Unique counts after V assignment, cross-donor analysis, and filtering on CDR L3 length (italics) are shown for reference only. 2
3 Table S4. Crystallographic Data Collection and Refinement Statistics, Related to Figure 5 d0dg5:.h0+ 07.O /.L0+07.O H0+ 07.O /.L0+07.O H03+06.D H08.F H5.F b Q842.d2: 8 PDB accession code 4XVS 4XVT 4SQ 4SR 4SS 4XNZ 4XMP 4XNY Data collection Space group P2 2 2 P2 2 2 P2 2 2 P2 2 2 P2 2 2 P2 2 2 P2 2 2 P4 3 Cell constants a, b, c (Å) α,, ( ) Q842.d2: 8c 67.6, 69.3, , 67.8, , 78.9, , 68., , 67.6, ,89.4, , 82.5, , 2.5, 68.7 Wavelength (Å) Resolution (Å) ( )* ( ) ( ) ( ) ( )* ( ) ( ) ( ) R merge 5.2 (90.0) 3.7 (99.0).3 (5.5) 5.6 (53.0) 9.7 (52.0) 9.3 (56.6) 8.8 (64.3) 7.8 (55.6) R pim 6.7 (56.) 5.3 (53.2) 7.6 (63.4) 7.4 (38.8) 4.8 (35.4) I / I 9.5 (.) 3.0 (.08) 2.4 (.6) 8.8 (.3) 4.4 (.6) 2.4 (.8) 25. (.9) 6.8 (.9) Completeness (%) 92.8 (88.6) 99.9 (99.9) 96.3 (80.4) 93.6 (53.7) 97.2 (82.8) 86.0 (50.0) 97.9 (89.7) 99. (94.3) Redundancy 7.0 (5.3) 9.6 (6.2) 3.7 (.8) 5.0 (.7) 4.7 (2.4) 5.8 (3.4) 5.9 (4.2) 3.7 (3.0) Refinement Resolution (Å) Unique reflections 69,542 97,827 36,988 4,552 4,88 34,907 88,3 44,409 R work / R free (%) 9.4/ / / / / / / /2.7 No. atoms Protein ,038 6,048 6,09 6,032 7,958 6,02 6,027 Ligand/ion Water B-factors (Å 2 ) Protein gp20-only Fv-only F CH-CL -only Ligand/ion Water R.m.s. deviations Bond lengths (Å) Bond angles ( ) Ramachandran Favored regions (%) Allowed regions (%) Disallowed regions (%) *Values in parentheses are for highest-resolution shell 3
4 Table S5. Structural Comparison of Antibody Heavy and Light Chains and Binding Surfaces, Related to Figure 7 A NIH b.H D c.H08.F H5.F NIH b H D c H08.F B VRC-PG04 3BNC7 2A2 VRC-CH3 VRC-PG20 VRC23 VRC-PG BNC A VRC-CH VRC-PG VRC H5.F C CDR H CDR H2 CDR H3 FR 3 Light Chain Total NIH Average H03+06.D Average
5 c H08.F Average H5.F (A) C -RMSDs (Å) were calculated after aligning framework regions of heavy chain (residues 3-26, 36-49, 65-76, 78-94, and 03-3, first row of each cell) and light chain (residues 3-23, 35-49, 56-88, and 98-02, italicized bottom row of each cell) with the corresponding regions of antibodies of donor 45. RMSDs within clades were colored in red, blue, and purple for 0+07 clade, clade, and 08 clade, respectively. (B) Cα-RMSDs (Å) were calculated after aligning framework regions of heavy chain (residues 3-26, 36-49, 65-76, 78-94, and 03-3, first row of each cell) and light chain (residues 3-23, 35-49, 56-88, and 98-02, italicized bottom row of each cell) with the corresponding regions of antibodies from donor 45 and other donors. RMSDs within clades were colored in red, blue, and purple for 0+07 clade, clade, and 08 clade, respectively. RMSDs within donor 45 antibodies were colored in red..h03+06.d-00739,.h08.f-7225, and.h5.f-8597 were heavy chain NGS reads that were expressed and crystallized together with the light chain. (C) Binding surfaces on gp20 by donor 45 antibodies..h03+06.d-00739,.h08.f- 7225, and.h5.f-8597 are heavy chain NGS reads that were expressed and crystallized together with the light chain. 5
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