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 80 0260.v5.c36 A 0.328 0.849 T255-34 AG 22.5 >50 257-2.4 C 0.85 0.50 0330.v4.c3 A 0.47 0.346 T257-3 AG.25 4.99 25925-2.22 C 0.058 0.69 0439.v5.c A 0.779 2.44 T266-60 AG 0.596 2.5 269-2.48 C 0.32 0.352 3365.v2.c20 A 0.065 0.25 T278-50 AG >50 >50 368.V4.C0 C 0.28 0.582 345.v.c A 0.46 0.469 T280-5 AG 0.027 0.08 3637.V5.C3 C 0.09 0.289 378.v3.c A >50 >50 T33-7 AG 0.020 0.045 3873.V.C24 C.5 4.83 398-F_F6_20 A 0.50.0 3988.25 B 0.30 0.34 6322.V4.C C >50 >50 BB20.B42 A 0.340 0.757 5768.04 B 0.59 0.548 647.V.C6 C >50 >50 BB539.2B3 A 0.072 0.72 60.0 B 0.020 0.060 663.V3.C0 C 0.964 5.59 BI369.9A A 0.096 0.299 6535.3 B 0.088 0.328 6644.V2.C33 C 0.02 0.054 BS208.B A 0.027 0.00 765.8 B 3.6 4.8 6785.V5.C4 C 0.2 0.344 KER2008.2 A 0.680 2.60 45_0dG5 B 0.004 0.02 6838.V.C35 C 0.48 0.540 KER208. A.29 3.78 89.6 B 0.094 0.335 96ZM65.02 C 0.20 0.33 KNH209.8 A 0.096 0.340 AC0.29 B 0.570 2.3 BR025.9 C 5.59 43.9 MB20.A A 0.280 0.625 ADA B 0.037 0.25 CAP20.E8 C >50 >50 MB539.2B7 A 0.62 0.478 BaL.0 B 0.03 0.08 CAP244.D3 C 0.86 0.566 MI369.A5 A 0.49 0.526 BaL.26 B 0.02 0.032 CAP45.G3 C 0.90 0.550 MS208.A A 0.479 2.35 BG68.0 B 0.75 0.37 CNE30 C 0.237 0.662 Q23.7 A 0.085 0.260 BL0 B >50 >50 CNE3 C 0.42 0.50 Q259.7 A 0.047 0.29 BR07 B 0.27 0.450 CNE53 C 0.05 0.82 Q769.d22 A 0.044 0.25 BX08.6 B 0.079 0.26 CNE58 C 0.038 0.08 Q842.d2 A 0.033 0.076 CAAN.A2 B 0.333.3 Du23.06 C 0.47.590 QH209.4M.A2 A 0.045 0.6 CNE0 B 0.099 0.295 Du5.02 C 0.69 0.529 RW020.2 A 0.289 0.760 CNE2 B 0.077 0.245 Du56.2 C 0.062 0.79 UG037.8 A 0.042 0.3 CNE4 B 0.035 0.2 Du72.7 C >50 >50 330.V.C24 AC 0.062 0.58 CNE4 B 0.53 0.592 Du422.0 C 6.8 >50 3589.V.C4 AC 0.093 0.295 CNE57 B 0.074 0.202 MW965.26 C 0.070 0.427 6540.v4.c AC >50 >50 HO86.8 B >50 >50 SO8.8 C 0.022 0.08 6545.V4.C AC >50 >50 HT593. B 0.052 0.227 TV.29 C >50 >50 085.V3.C3 ACD 0.07 0.99 HXB2 B 0.02 0.035 TZA25.7 C >50 >50 6095.V.C0 ACD 0.422 2.80 JR-CSF B 0.05 0.302 TZBD.02 C 0.00 0.030 3468.V.C2 AD.84 >50 JR-FL B 0.006 0.08 ZA02.29 C 0.080 0.99 Q68.a2 AD 0.9 0.400 MN.3 B 0.02 0.047 ZM06.9 C 0.058 0.36 Q46.e2 AD 0.35 0.823 PVO.04 B 0.04 0.24 ZM09.4 C 0.069 0.26 620345.c AE >50 >50 QH055.0 B 0.453.64 ZM35.0a C 0.27 0.509 BJOX009000.02.4 AE 0.743 2.07 QH0692.42 B 0.350.6 ZM76.66 C 0.400 >50 BJOX00000.06.2 AE 0.622 2.62 REJO.67 B 0.050 0.37 ZM97.7 C 0.207 0.792 BJOX025000.0. AE 0.4 0.275 RHPA.7 B 0.065 0.76 ZM24.5 C 0.397.27 BJOX028000.0.3 AE 0.02 0.09 SC422.8 B 0.057 0.50 ZM25.8 C 0.050 0.77 C080.c3 AE 0.243.30 SF62 B 0.033 0.097 ZM249. C 0.08 0.28 C20.c AE 0.08 0.352 SS96.0 B 0.063 0.8 ZM53.2 C 0.2.0 C3347.c AE 0.024 0.080 THRO.8 B.3 7.85 ZM55.28a C 0.048 0.43 C48.09 AE 0.057 0.53 TRJO.58 B 0.49 0.373 3326.V4.C3 CD >50 >50 CM244.ec AE 0.07 0.059 TRO. B 0.088 0.267 3337.V2.C6 CD 0.048 0.22 CNE3 AE 0.5 0.328 WITO.33 B 0.060 0.78 387.v2.c59 CD >50 >50 CNE5 AE 0.292 0.930 Yu2 B 0.034 0.080 982.E6. D 0.5 0.60 CNE55 AE 0.02 0.296 CH038.2 BC 0.242 0.65 23965.c D 7.7 >50 CNE56 AE 0.94 0.84 CH070. BC >50 >50 247-23 D 0.066 0.25 CNE59 AE 0.23 0.536 CH7.4 BC 0.037 0.6 306.v5.c45 D 0.23 0.82 CNE8 AE 0.55 0.397 CH8.2 BC 0.050 0.54 5728.vrc5 D >50 >50 M0238 AE 0.335.02 CNE5 BC 0.078 0.324 6405.v4.c34 D 0.485.22 R66.c AE 0.826.73 CNE9 BC 0.023 0.076 A03349M.vrc4a D.24 3.79 R284.c4 AE 0.07 0.75 CNE20 BC 0.040 0.098 A0742M.vrc2 D 0.09 0.35 R3265.c6 AE 0.085 0.274 CNE2 BC 0.073 0.209 NKU3006.ec D 0.587.57 TH023.6 AE 0.024 0.087 CNE40 BC 0.032 0.30 UG024.2 D 0.604 2.75 TH966.8 AE 0.050 0.72 CNE7 BC 0.040 0.25 P0402.c2. G 0.068 0.253 TH976.7 AE 0.4 0.34 286.36 C 0.27 0.744 P98.C5.3 G 0.7 0.368 235-47 AG 0.06 0.256 288.38 C 0.66 0.530 X93.c G 0.063 0.78 242-4 AG >50 >50 003095-2. C 0.05 0.078 X254.c3 G 0.249 0.75 263-8 AG 0.03 0.42 00428-2.42 C 0.009 0.022 X632.S2.B0 G 2.88 >50 269-2 AG 0.56.42 0077_V.C6 C >50 >50 X2088.c9 G >50 >50 27- AG 0.07 0.38 00836-2.5 C 0.05 0.037 928-28 AG 0.64 0.675 092.V2.C4 C 0.52 0.40 DJ263.8 AG 0.04 0.068 6055-2.3 C 0.04 0. T250-4 AG >50 >50 682.22 C 0.352 2.33 T25-8 AG.3 4.44 6936-2.2 C 0.078 0.207 T253- AG 0.577 2.27 2570-2.43 C 0.073 0.97
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) 767 656 79 638 60 647 629 530 686 583,000 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 932,697 304,968 280,4 529,389 39,684 377,09 220,926 476,045 267,953 506,209 4,25,004 total heavy with length and V unique* heavy with length and V total crossdonor positives (XD+) 66,038 304,944 280,088 529,52 39,67 376,939 24,95 475,999 267,902 506,54 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 49,835 260,253 unique* XD+ 5,760 766 4,20,847 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* 47 50 35 0 06 47 328 206 360 206,886 final curated 9 92 68 54 70 73 88 4 93 98,04 raw light 89,850 377,954 456,794 685,467 364,358 509,46 463,929 644,062 363,276 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 ) 89,65 377,99 455,930 685,405 364,340 509,44 463,862 64,637 362,433 36,34 4,4,76 78,402 52,043 95,404 23,380 48,2 64,796 70,487 284,903 55,439 6,023 789,088 6,363 56 4,329 8,279,3 8,853 4,947 8,323 5,55 6,475 54,398 2,45 275,067 324 329 788 70 2,987 875 30 9,80 77 208,322 7,84 640 3,994 3,072 3,36 3,245 4,892 28,500 08 47 738 5,76 273 2,903 2,335,797 2,39 3,786 9,987 ORF unique* 32 42 55 22 70 0 87 75 38 533 final curated 0 3 39 53 22 66 92 79 68 32 492 * 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
Table S4. Crystallographic Data Collection and Refinement Statistics, Related to Figure 5 d0dg5:.h0+ 07.O-86353 /.L0+07.O- 0653.H0+ 07.O-86353 /.L0+07.O- 0653.H03+06.D- 00739.H08.F- 7225.H5.F- 8597 6b 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, 200.6 64.6, 67.8, 99.2 66., 78.9, 94.2 65.6, 68., 204. 55.3, 67.6, 266.7 68.3,89.4, 29.9 69.7, 82.5, 63. 2.5, 2.5, 68.7 Wavelength (Å).0000.0000.0000.0000.0000.0000.0000.0000 Resolution (Å) 50.0-.90 50.0-.70 50.00-2.40 50.0-3.20 50.00-3.40 39.90-3.39 35.50-.78 33.69-2.30 (.97-.90)* (.76-.70) (2.44-2.40) (3.26-3.20) (3.46-3.40)* (3.5-3.39) (.85-.78) (2.38-2.30) 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).90.70 2.40 3.20 3.40 3.40.78 2.30 Unique reflections 69,542 97,827 36,988 4,552 4,88 34,907 88,3 44,409 R work / R free (%) 9.4/2.4 8.7/22.5 2.9/25.8 26.0/28.6 26./29.9 24.2/28.9 6./9.3 8.2/2.7 No. atoms Protein 6045 6,038 6,048 6,09 6,032 7,958 6,02 6,027 Ligand/ion 729 772 54 54 55 366 66 54 Water 63 632 26 0 0 0 63 206 B-factors (Å 2 ) Protein 37.6 42.9 56. 02.4 0.5 35.3 45.0 55.9 gp20-only 4. 43.0 57.5 8.4 05.7 Fv-only 37.3 4.9 52.2 92.0 90.2 F CH-CL -only 3.0 37.5 76. 50.9 34.6 Ligand/ion 73.2 73.9 63.5 00. 27.9 78.30 58.2 70.6 Water 46.4 49.3 48.7 - - - 47.4 50.0 R.m.s. deviations Bond lengths (Å) 0.007 0.00 0.003 0.004 0.003 0.007 0.009 0.003 Bond angles ( ).02.9 0.737 0.97 0.879.70.60 0.833 Ramachandran Favored regions (%) 96.5 96.5 95.7 90.5 90.9 90.5 98.0 97.0 Allowed regions (%) 3.4 3.4 4.3 8.6 7.4 7.6.9 2.7 Disallowed regions (%) 0. 0. 0 0.9.7.9 0. 0.3 *Values in parentheses are for highest-resolution shell 3
Table S5. Structural Comparison of Antibody Heavy and Light Chains and Binding Surfaces, Related to Figure 7 A NIH46 3 6 6b.H03+06. D-00739 8 8c.H08.F- 7225.H5.F- 8597 0.459 0.363.42 0.64.48 0.953 0.695.653 2.408.056.028.04 0.923 0.895 0.598 0.46 0.664 0.473 NIH45-46.48 0.68.457.07 0.73.659 2.364.046 0.968.038 0.877 0.9 0.663 0.387 0.672 0.378 3 0.609 0.83.067.58 2.287.26 0.943 0.837 0.892 0.692.469 0.734.486 0.699 6.93.239 2.40.097.07.074.529.023.44.0.463.023 6 b.87 0.888.086 0.969 0.98 0.679 0.83 0.828 0.832 0.86.H03+06. D-00739 2.579.26 2.539 0.978.762 0.522.76 0.53 8 0.39 0.67 0.738.006 0.765 8 c 0.68 0.888 0.674 0.935.H08.F -7225 0.505 0.407 B VRC-PG04 3BNC7 2A2 VRC-CH3 VRC-PG20 VRC23 VRC-PG04.92 0.723 3BNC7.82.868 0.959 0.908 2A2 0.688 0.938.76.064.047.26 VRC-CH3.33.047 2.009.223 0.967.008.026 0.504 VRC-PG20.003.065.783 0.765.30.442.358.426.92 0.504 VRC23 0.585.049.78 0.52.237 0.799.056.032.7.26 0.596 0.44 3.42.756 2.28.43.89.674.46 0.64 0.848.06 0.787 0.775.255 0.755 6.48.79 2.7.425.937.573.47 0.953.007.032 0.958 0.847.344 0.963 8.028 0.989.875 0.688.297 0.677 0.833.04 0.792.43 0.96 0.945.286.008.H5.F-8597 0.664.086.769 0.687.307 0.97 0.658 0.473 0.705 0.986.22.029.464.3 C CDR H CDR H2 CDR H3 FR 3 Light Chain Total 34.5 563 53.7 40.7 369 260.9 NIH46 57. 669.5 360.9 66.4 92.4 446.3 Average 45.8 66.3 257.3 53.6 280.7 353.6 3 83.6 659.4 43. 76.5 336.9 399.5 6 68 630.7 48.9 76.5 335.2 359.3.H03+06.D-00739 69 665.2 03.2 270.7 332.5 440.6 Average 73.5 65.7 3.7 207.9 334.8 399.8 4
8 6.2 50.2 456.7 20.5 425.5 565. 8c 57. 553.6 46. 68.4 370.4 465.6.H08.F-7225 33.9 558.4 483.9 59.8 229.8 365.8 Average 50.7 537.7 452.2 82.9 34.9 465.5.H5.F-8597 35.8 608.9 98.9 44 328.6 26.2 (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, 03+06 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, 03+06 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